X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details ammonium sulfate, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.26 α = 90
b = 52.74 β = 90
c = 83.86 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Collimating mirror optics, double slit monochromator 2000-08-24
Diffraction Radiation
Monochromator Protocol
SI 111 Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 1.10002 NSLS X8C

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
2.13 100 94.0 -- 0.048 -- 2.9 69333 69333 0.0 -3.0 21.5
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)
2.13 2.18 73.3 -- 0.194 5.2 2.7 3610

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 2.12 8.97 -- 0.0 36074 36074 1797 96.2 -- -- 0.228 0.273 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 2.12 2.25 -- 264 5163 0.314 0.324 0.02 87.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 34.6
Anisotropic B[1][1] -8.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 18.56
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.564
c_scbond_it 1.82
c_mcangle_it 1.982
c_mcbond_it 1.276
c_improper_angle_d 1.04
c_dihedral_angle_d 17.6
c_bond_d 0.007
c_angle_deg 1.058
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2201
Nucleic Acid Atoms 1628
Heterogen Atoms 40
Solvent Atoms 330

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
GLRF Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
GLRF model building
TRUNCATE data reduction
DENZO data collection