X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 295.0
Details sodium-potassium buffer , pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.29 α = 90
b = 58.97 β = 90
c = 88.63 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Mirrors 2002-01-27
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 1.00000 APS 5ID-B

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
1.75 19 98.3 0.053 -- -- 5.7 22129 22129 0.0 -3.0 --
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)
1.75 1.81 97.7 0.414 -- 3.5 5.1 2162

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 1.75 19.0 0.0 0.0 22481 21232 2061 94.4 -- -- 0.171 0.198 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 1.75 1.81 1885 181 -- 0.2915 0.2996 -- 85.14
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, individual B values refined
Mean Isotropic B 20.5
Anisotropic B[1][1] 2.831
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.443
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.612
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.612
c_mcangle_it 2.126
c_scbond_it 2.625
c_mcbond_it 1.665
c_improper_angle_d 0.89
c_dihedral_angle_d 20.9
c_angle_deg 1.4
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2026
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 367

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection