X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.22 α = 90
b = 48.22 β = 90
c = 63.28 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER APEX II multi-layer optics 2005-01-20
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
1.75 17.98 99.8 0.0301 0.0199 -- 10.6 14741 14710 0.0 0.0 33.1
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)
1.75 1.84 99.3 0.2839 0.2574 4.05 3.43 2016

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 1.8 17.0 0.0 0.0 13483 12753 1272 94.61 0.23 0.203 0.198 0.255 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 1.8 1.846 1091 98 749 0.251 0.383 -- 85.3
X Ray Diffraction 1.846 1.896 1030 66 -- 0.232 0.31 -- 87.241
X Ray Diffraction 1.896 1.95 1027 94 -- 0.198 0.255 -- 89.496
X Ray Diffraction 1.95 2.01 979 83 -- 0.218 0.327 -- 91.183
X Ray Diffraction 2.01 2.075 949 78 -- 0.215 0.299 -- 93.915
X Ray Diffraction 2.075 2.146 934 76 -- 0.206 0.284 -- 94.639
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.909
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 18.093
r_angle_refined_deg 2.08
r_chiral_restr 0.157
r_bond_refined_d 0.009
r_mcangle_it 3.159
r_scangle_it 7.239
r_mcbond_it 2.056
r_dihedral_angle_1_deg 7.47
r_dihedral_angle_4_deg 20.903
r_scbond_it 5.07
r_dihedral_angle_2_deg 29.248
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1024
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 81

Software

Software
Software Name Purpose
SAINT data scaling
PHASER phasing
DM phasing version: 6.0.99d
REFMAC refinement version: 5.5.0017
PDB_EXTRACT data extraction version: 3.005
APEX data collection
SAINT data reduction