X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 277.0
Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.3 α = 90
b = 102.57 β = 90
c = 139.54 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 85
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER SMART 6000 Mirrors 2010-08-13
Diffraction Radiation
Monochromator Protocol
Osmic Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.54 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.67 57.69 99.5 0.0532 0.0532 -- 5.78 94375 93933 -3.0 -3.0 17.5
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.67 1.68 99.4 0.375 0.375 2.5 3.25 13251

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.67 57.689 0.0 0.0 -- 93836 4671 95.18 -- 0.1646 0.1633 0.1905 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.67 1.684 -- 22 402 0.2718 0.3601 -- 13.0
X Ray Diffraction 1.684 1.7038 -- 93 1678 0.251 0.3191 -- 55.0
X Ray Diffraction 1.7038 1.7246 -- 163 3009 0.2393 0.2909 -- 98.0
X Ray Diffraction 1.7246 1.7464 -- 175 3058 0.2221 0.2456 -- 99.0
X Ray Diffraction 1.7464 1.7694 -- 157 3088 0.211 0.2598 -- 99.0
X Ray Diffraction 1.7694 1.7936 -- 142 3059 0.2015 0.2284 -- 100.0
X Ray Diffraction 1.7936 1.8193 -- 144 3093 0.1937 0.2796 -- 99.0
X Ray Diffraction 1.8193 1.8464 -- 173 3045 0.1849 0.2313 -- 99.0
X Ray Diffraction 1.8464 1.8753 -- 148 3083 0.1782 0.2136 -- 99.0
X Ray Diffraction 1.8753 1.906 -- 167 3026 0.1706 0.2003 -- 99.0
X Ray Diffraction 1.906 1.9389 -- 188 3062 0.163 0.2122 -- 99.0
X Ray Diffraction 1.9389 1.9742 -- 187 2996 0.1646 0.2027 -- 99.0
X Ray Diffraction 1.9742 2.0121 -- 172 3100 0.1688 0.188 -- 99.0
X Ray Diffraction 2.0121 2.0532 -- 166 3038 0.1616 0.1995 -- 99.0
X Ray Diffraction 2.0532 2.0978 -- 148 3095 0.1652 0.2052 -- 99.0
X Ray Diffraction 2.0978 2.1467 -- 180 3076 0.1583 0.2022 -- 99.0
X Ray Diffraction 2.1467 2.2003 -- 134 3105 0.154 0.193 -- 100.0
X Ray Diffraction 2.2003 2.2598 -- 175 3094 0.1471 0.1825 -- 100.0
X Ray Diffraction 2.2598 2.3263 -- 182 3108 0.1452 0.1826 -- 100.0
X Ray Diffraction 2.3263 2.4014 -- 169 3106 0.1478 0.1912 -- 100.0
X Ray Diffraction 2.4014 2.4872 -- 148 3127 0.1515 0.1711 -- 100.0
X Ray Diffraction 2.4872 2.5868 -- 166 3121 0.1548 0.1829 -- 100.0
X Ray Diffraction 2.5868 2.7046 -- 175 3128 0.1518 0.1785 -- 100.0
X Ray Diffraction 2.7046 2.8471 -- 157 3134 0.156 0.1742 -- 100.0
X Ray Diffraction 2.8471 3.0255 -- 157 3174 0.1524 0.1753 -- 100.0
X Ray Diffraction 3.0255 3.2591 -- 162 3163 0.1597 0.1556 -- 100.0
X Ray Diffraction 3.2591 3.587 -- 148 3182 0.1544 0.179 -- 100.0
X Ray Diffraction 3.587 4.106 -- 173 3191 0.1455 0.1555 -- 100.0
X Ray Diffraction 4.106 5.1726 -- 148 3236 0.1525 0.1669 -- 100.0
X Ray Diffraction 5.1726 57.7238 -- 152 3388 0.1901 0.2199 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.1499
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2124
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.9374
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.073
f_dihedral_angle_d 12.712
f_angle_d 1.152
f_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6162
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1060

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
PROTEUM PLUS Data Reduction (intensity integration)
PROTEUM PLUS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHASER model building
PROTEUM version: PLUS data collection