X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 293.0
Details Na/K Phosphate, PEG 4000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69 α = 90
b = 98.57 β = 105.53
c = 89.35 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR -- -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.62 39.5 99.4 0.073 0.067 -- 6.1 36632 35267 -- -3.0 76.609
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)
2.62 2.74 96.4 0.496 0.453 3.2 5.9 5109

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 2.62 39.0 -- 0.0 36632 34900 1726 99.7 -- -- 0.221 0.258 same as 1e04
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 2.62 2.76 5254 234 -- 0.342 0.358 0.023 88.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Anisotropic B[1][1] -10.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -7.66
Anisotropic B[2][2] 20.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.27
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.1
c_bond_d 0.008
c_angle_deg 1.4
c_improper_angle_d 0.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.42
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6434
Nucleic Acid Atoms 0
Heterogen Atoms 173
Solvent Atoms 54

Software

Software
Software Name Purpose
MAR data collection
SCALA data scaling
MOLREP phasing
CNS refinement version: 1.0
MAR data reduction
CCP4 data scaling version: (SCALA)