X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 280.0
Details 1.5 M ammonium sulfate, 200 mM phosphate, 0.1 mM thiamine diphosphate, 1 mM magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.28 α = 90
b = 154.16 β = 90
c = 165.47 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Toroidal focusing mirror 2011-11-22
Diffraction Radiation
Monochromator Protocol
channel cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.979200 ESRF ID14-4

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
1.06 35 94.9 0.07 0.081 -- 3.38 645341 645341 0.0 -3.0 10.593
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)
1.06 1.13 93.2 0.52 -- 2.21 -- --

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
FOURIER SYNTHESIS 1.06 30.0 0.0 0.0 625966 645341 19361 91.6 -- 0.1271 0.1271 0.1505 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.8418
RMS Deviations
Key Refinement Restraint Deviation
s_from_restr_planes 0.037
s_approx_iso_adps 0.105
s_angle_d 310.0
s_bond_d 0.015
s_non_zero_chiral_vol 6.0
s_rigid_bond_adp_cmpnt 0.0
s_similar_adp_cmpnt 0.046
s_zero_chiral_vol 79.0
s_similar_dist 0.0
s_anti_bump_dis_restr 0.087
Coordinate Error
Parameter Value
Number Disordered Residues 285.0
Occupancy Sum Hydrogen 8946.42
Occupancy Sum Non Hydrogen 11037.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9048
Nucleic Acid Atoms 0
Heterogen Atoms 225
Solvent Atoms 1899

Software

Software
Software Name Purpose
XSCALE data scaling
SHELX refinement
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
XDS data reduction
PHENIX phasing
SHELXL refinement