X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.2
Temperature 277.0
Details 50% PEG 300, 0.2M Sodium chloride, 0.1M Sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.1 α = 90
b = 139.1 β = 90
c = 109.62 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2007-02-11
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.79887 SLS X10SA

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
2.51 50 99.7 0.061 -- -- 7.5 42245 42245 0.0 0.0 67.6
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)
2.51 2.66 98.5 0.621 -- 3.39 7.5 6634

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 2.51 29.361 -- 0.0 42226 42226 2127 99.63 0.177 0.177 0.175 0.212 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 2.51 2.57 3016 151 2865 0.3 0.294 -- 96.82
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 28.714
Anisotropic B[1][1] 1.05
Anisotropic B[1][2] 0.53
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.58
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.067
r_bond_refined_d 0.01
r_nbd_other 0.178
r_bond_other_d 0.002
r_nbtor_other 0.084
r_dihedral_angle_4_deg 19.987
r_mcangle_it 0.708
r_angle_other_deg 0.915
r_nbd_refined 0.213
r_xyhbond_nbd_refined 0.143
r_mcbond_other 0.072
r_gen_planes_other 0.001
r_angle_refined_deg 1.306
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.191
r_nbtor_refined 0.174
r_symmetry_vdw_refined 0.112
r_scangle_it 1.924
r_mcbond_it 0.412
r_scbond_it 1.183
r_symmetry_vdw_other 0.255
r_dihedral_angle_2_deg 34.782
r_dihedral_angle_1_deg 5.338
r_dihedral_angle_3_deg 15.527
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5155
Nucleic Acid Atoms 0
Heterogen Atoms 104
Solvent Atoms 150

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
XDS data reduction
XDS data scaling