X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 289.0
Details 0.2 M sodium fluoride, 22.5% PEG3350, VAPOR DIFFUSION, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.17 α = 90
b = 114.64 β = 90
c = 69.5 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRRORS 2012-11-11
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID

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
2.54 50 98.9 0.108 -- -- 5.0 -- 33838 -- -- 34.9
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)
2.54 2.58 97.2 0.571 -- 2.3 4.6 1632

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 2.54 46.96 -- 0.0 -- 31612 1606 92.48 -- 0.2366 0.2347 0.2723 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 2.54 2.608 -- 70 1337 0.26 0.292 -- 57.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.2763
Anisotropic B[1][1] -1.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.31
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.184
r_chiral_restr 0.07
r_bond_other_d 0.007
r_dihedral_angle_3_deg 15.59
r_angle_refined_deg 1.356
r_dihedral_angle_2_deg 36.453
r_gen_planes_refined 0.008
r_dihedral_angle_4_deg 15.009
r_bond_refined_d 0.013
r_dihedral_angle_1_deg 5.963
r_gen_planes_other 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6787
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 94

Software

Computing
Computing Package Purpose
HKL3000 Data Reduction (intensity integration)
HKL3000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
MOLREP molecular replacement
REFMAC5 refinement
pdb_extract version: 3.11 data extraction
HKL data reduction