X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.96 α = 90
b = 103.07 β = 90
c = 138.83 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 Osmic Mirrors 2010-07-14
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
2.2 100 99.9 0.0557 0.0557 -- 11.14 44573 44527 -3.0 -3.0 23.8
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)
2.2 2.29 99.2 0.311 0.311 3.34 6.41 4959

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 2.2 42.217 -- 1.34 -- 44444 2149 99.89 -- 0.1747 0.1728 0.2116 --
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 2.2 2.2512 -- 132 2747 0.2163 0.3016 -- 99.0
X Ray Diffraction 2.2512 2.3075 -- 163 2776 0.2065 0.2388 -- 100.0
X Ray Diffraction 2.3075 2.3699 -- 144 2753 0.2086 0.2327 -- 100.0
X Ray Diffraction 2.3699 2.4396 -- 155 2799 0.1945 0.2692 -- 100.0
X Ray Diffraction 2.4396 2.5183 -- 138 2767 0.1953 0.2221 -- 100.0
X Ray Diffraction 2.5183 2.6083 -- 147 2803 0.185 0.218 -- 100.0
X Ray Diffraction 2.6083 2.7127 -- 148 2786 0.1798 0.2083 -- 100.0
X Ray Diffraction 2.7127 2.8362 -- 148 2797 0.1784 0.2239 -- 100.0
X Ray Diffraction 2.8362 2.9857 -- 118 2820 0.1771 0.2031 -- 100.0
X Ray Diffraction 2.9857 3.1727 -- 165 2781 0.1751 0.2356 -- 100.0
X Ray Diffraction 3.1727 3.4175 -- 133 2833 0.1699 0.2163 -- 100.0
X Ray Diffraction 3.4175 3.7613 -- 141 2856 0.1579 0.1853 -- 100.0
X Ray Diffraction 3.7613 4.3051 -- 143 2852 0.1396 0.1602 -- 100.0
X Ray Diffraction 4.3051 5.4221 -- 144 2897 0.143 0.1914 -- 100.0
X Ray Diffraction 5.4221 42.2252 -- 130 3028 0.1852 0.2082 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.7269
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.0667
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7936
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 12.909
f_angle_d 1.039
f_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.62
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6198
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 743

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