X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 296.0
Details 25% PEG 2000, 0.1 M MES, 0.45 M MAGNESIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 273.52 α = 90
b = 273.52 β = 90
c = 273.52 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
CCD MARMOSAIC 225 mm CCD DCM WITH CRYO-COOLED. 1ST CRYSTAL SAGITTALLY BENT. 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR. 2010-07-28
Diffraction Radiation
Monochromator Protocol
A DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-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
2.3 55.8 100.0 0.105 -- -- 8.7 39388 39388 0.0 0.0 36.3
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)
2.3 2.4 100.0 0.249 -- 6.5 8.1 5637

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 2.3 55.8 -- 0.0 39388 39388 1978 100.0 -- 0.17394 0.17269 0.19685 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 2.3 2.4 5637 123 2474 0.21 0.246 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.166
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.017
r_chiral_restr 0.121
r_dihedral_angle_4_deg 15.075
r_dihedral_angle_3_deg 15.736
r_dihedral_angle_2_deg 38.973
r_dihedral_angle_1_deg 7.018
r_angle_refined_deg 1.428
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3026
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 320

Software

Computing
Computing Package Purpose
MXDC Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
Phaser model building
MXDC data collection