X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details Protein at 10 mg/mL in the buffer: 20mM Tris pH 8.0, 150 mM NaCl, 10% Glycerol, 1mM DTT, 1mM EDTA. mixed 1:1 with well solution containing: 200 mM CaAcetate, 24% PEG 400, 100 mM Sodium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.27 α = 90
b = 74.27 β = 90
c = 119.14 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 140
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ Source: 3.3 Undulator (Undulator A) Monochromator Type: Diamond(111) Energy Range 4.7-28 keV Resolution ( E/E) 1 x 10 -4 Flux (photons/sec) 2 x 1012 @12.4 keV Beam Size (HxV) Focused 80 m x 70 m 2012-02-10
Diffraction Radiation
Monochromator Protocol
Diamond(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97 APS 31-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
1.95 119.14 100.0 -- 0.057 -- 7.6 47060 47060 0.0 0.0 30.9
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)
1.95 2.05 100.0 0.462 0.462 1.6 7.5 6844

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 1.95 19.66 -- 0.0 -- 46878 2376 99.96 -- 0.1824 0.1811 0.2065 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 1.95 2.0 -- 185 3254 0.1864 0.2218 -- 99.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.776
Anisotropic B[1][1] -1.258
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.258
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.516
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_omega_torsion 3.22
t_other_torsion 16.96
t_angle_deg 1.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.194
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3418
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 412

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
BUSTER-TNT refinement version: BUSTER 2.11.2
PDB_EXTRACT data extraction version: 3.11
SPEC data collection
PROCESS data reduction
AMoRE phasing
BUSTER refinement version: 2.11.2