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 = 59.71 α = 90
b = 102.99 β = 90
c = 139.34 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 2010-08-07
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
1.95 100 99.9 0.0844 0.0844 -- 5.76 63173 63086 -3.0 -3.0 17.9
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)
1.95 2.05 99.0 0.4078 0.4078 2.32 3.78 8303

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 1.954 51.653 -- 1.34 -- 62990 3112 99.9 -- 0.1634 0.1614 0.2036 --
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 1.954 1.9846 -- 153 2642 0.2289 0.2738 -- 98.0
X Ray Diffraction 1.9846 2.0171 -- 150 2666 0.2092 0.2464 -- 100.0
X Ray Diffraction 2.0171 2.0519 -- 163 2666 0.1885 0.233 -- 100.0
X Ray Diffraction 2.0519 2.0892 -- 132 2679 0.1739 0.2615 -- 100.0
X Ray Diffraction 2.0892 2.1294 -- 132 2713 0.1745 0.2102 -- 100.0
X Ray Diffraction 2.1294 2.1728 -- 154 2643 0.1623 0.2162 -- 100.0
X Ray Diffraction 2.1728 2.2201 -- 126 2729 0.1568 0.2279 -- 100.0
X Ray Diffraction 2.2201 2.2717 -- 147 2669 0.1521 0.218 -- 100.0
X Ray Diffraction 2.2717 2.3285 -- 160 2690 0.1558 0.2359 -- 100.0
X Ray Diffraction 2.3285 2.3915 -- 142 2720 0.1586 0.1866 -- 100.0
X Ray Diffraction 2.3915 2.4619 -- 138 2682 0.154 0.2321 -- 100.0
X Ray Diffraction 2.4619 2.5413 -- 144 2705 0.1611 0.2086 -- 100.0
X Ray Diffraction 2.5413 2.6321 -- 137 2716 0.157 0.2358 -- 100.0
X Ray Diffraction 2.6321 2.7375 -- 141 2721 0.1562 0.1952 -- 100.0
X Ray Diffraction 2.7375 2.8621 -- 148 2724 0.1558 0.1974 -- 100.0
X Ray Diffraction 2.8621 3.013 -- 112 2725 0.1543 0.1994 -- 100.0
X Ray Diffraction 3.013 3.2017 -- 162 2722 0.1646 0.2012 -- 100.0
X Ray Diffraction 3.2017 3.4489 -- 126 2770 0.1584 0.1905 -- 100.0
X Ray Diffraction 3.4489 3.7959 -- 141 2739 0.1548 0.187 -- 100.0
X Ray Diffraction 3.7959 4.3449 -- 138 2782 0.1354 0.1566 -- 100.0
X Ray Diffraction 4.3449 5.4732 -- 139 2814 0.1492 0.1752 -- 100.0
X Ray Diffraction 5.4732 51.6711 -- 127 2961 0.1873 0.201 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.8311
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3769
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.4542
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.074
f_dihedral_angle_d 12.937
f_angle_d 1.065
f_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6168
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 942

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