X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 282.0
Details PEG 6000, Potassium phosphate, L-citrulline, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.24 α = 90
b = 76.37 β = 109.74
c = 82.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- --
IMAGE PLATE MARRESEARCH -- 1997-06-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --
SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25

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 99 97.1 0.083 -- -- -- 59662 59662 -- 0.0 --
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)
2.0 2.03 90.4 0.219 -- 4.6 -- --

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
MIR 2.0 19.95 -- 1.0 -- 58076 2933 94.6 -- 0.1861 0.186 0.227 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 2.0 2.13 -- 457 8613 0.24 0.313 0.015 88.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.9
Anisotropic B[1][1] 4.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.03
Anisotropic B[2][2] -2.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.38
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.85
c_scbond_it 4.22
c_mcangle_it 3.73
c_mcbond_it 3.33
c_improper_angle_d 0.88
c_dihedral_angle_d 23.3
c_angle_deg 1.6
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6540
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 550

Software

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