X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Details 20MM K2HPO4, KH2PO4, 25MM POTASIUM MES OR SODIUM HEPES, PH 7.0 0.2 MM 2-MERCAPTOETHANOL, 3% PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.38 α = 90
b = 116.38 β = 90
c = 165.38 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU -- --
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.8 35 100.0 0.173 -- -- 19.0 -- 28327 -- -3.0 88.8

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
MIRAS 2.8 20.0 -- 0.0 -- 28454 2885 99.7 -- -- 0.214 0.28 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 2.8 2.97 -- 446 4199 0.399 0.442 0.021 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 70.8
Anisotropic B[1][1] -2.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.3
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.016
c_angle_deg 2.0
c_dihedral_angle_d 23.4
c_improper_angle_d 2.17
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.7
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6982
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 12

Software

Software
Software Name Purpose
PHASES phasing
CNS refinement version: 0.5
DENZO data reduction
SCALEPACK data scaling