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_improper_angle_d 0.82
c_dihedral_angle_d 24.1
c_angle_deg 1.4
c_bond_d 0.008
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

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
MolRep model building
SCALA data reduction
MAR data collection