X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 300.0
Details PEG 4000, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.99 α = 90
b = 123.13 β = 90
c = 37.93 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SIEMENS -- 1998-06-25
CCD CUSTOM-MADE -- 1998-09-21
Diffraction Radiation
Monochromator Protocol
graphite crystal SINGLE WAVELENGTH
graphite crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 0.979 APS 17-ID
SYNCHROTRON NSLS BEAMLINE X12C 0.95, 0.979, 0.978 NSLS X12C

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
1.6 27.65 76.5 -- 0.078 -- 4.8 55397 41788 -3.0 -- 10.7
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)
1.6 1.7 40.5 -- 0.173 2.88 4.02 --

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
MAD 1.8 27.65 -- 0.0 -- 41788 2100 88.1 0.202 0.202 0.202 0.24 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 1.8 1.91 -- 279 5503 0.211 0.268 0.016 74.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 12.1
Anisotropic B[1][1] 0.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.53
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.32
c_bond_d 0.006
c_angle_deg 1.5
c_dihedral_angle_d 18.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3728
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 623

Software

Computing
Computing Package Purpose
DENZO, SAINT Data Reduction (intensity integration)
SCALEPACK, SAINT Data Reduction (data scaling)
SOLVE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement