X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details 1.6 M Sodium Malonate, pH 5.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 253.26 α = 90
b = 253.26 β = 90
c = 253.26 γ = 90
Symmetry
Space Group F 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2006-08-24
Diffraction Radiation
Monochromator Protocol
VariMax-HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
3 19.84 99.9 -- -- -- 5.45 14420 14405 0.0 3.0 --
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 3.11 100.0 0.613 -- 1.8 -- --

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 19.84 -- 0.0 -- 14369 1442 99.85 -- 0.2939 0.2894 0.3337 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 3.001 3.077 -- 101 919 0.341 0.417 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.8717
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.361
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 39.701
r_angle_other_deg 0.948
r_chiral_restr 0.089
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_scbond_it 1.806
r_dihedral_angle_1_deg 7.413
r_dihedral_angle_4_deg 18.859
r_mcbond_other 0.092
r_scangle_it 3.251
r_angle_refined_deg 1.608
r_dihedral_angle_3_deg 21.148
r_mcbond_it 0.698
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2057
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 3

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
CrystalClear data reduction
CrystalClear data scaling