X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 2.25 M SODIUM MALONATE, PH 7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 137.9 α = 90
b = 206.59 β = 90
c = 174.69 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2011-11-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
3 30 99.5 0.03 -- -- 7.4 -- 49904 -- 2.0 --
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)
3.0 30.0 -- -- -- -- -- --

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 3.0 29.67 -- -- -- 47343 2536 99.37 -- 0.17861 0.17751 0.19933 RANDOM
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 3.0 3.077 -- 197 3447 0.295 0.287 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 74.664
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.023
r_angle_other_deg 1.57
r_dihedral_angle_1_deg 8.769
r_chiral_restr 0.14
r_dihedral_angle_2_deg 33.954
r_dihedral_angle_4_deg 22.938
r_angle_refined_deg 2.573
r_gen_planes_refined 0.011
r_bond_other_d 0.007
r_gen_planes_other 0.002
r_dihedral_angle_3_deg 19.831
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6180
Nucleic Acid Atoms 0
Heterogen Atoms 126
Solvent Atoms 12

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0029
XDS data reduction
XDS data scaling
PHASER phasing