X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details Na/Cacodylate, Ammonium Sulfate, PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.93 α = 90
b = 102.96 β = 99.4
c = 119.94 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
CCD ADSC QUANTUM 315 -- 2006-12-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU

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
2.5 50 93.8 -- 0.058 -- 3.6 -- 82592 -- -- 39.0
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)
2.5 2.59 67.4 -- 0.357 -- -- --

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 2.5 45.68 -- 0.0 -- 82571 4162 93.7 -- 0.226 0.226 0.268 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 2.5 2.66 -- 490 9979 0.367 0.419 0.019 71.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 63.3
Anisotropic B[1][1] 6.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -20.58
Anisotropic B[2][2] -9.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.34
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.3
c_scbond_it 1.88
c_dihedral_angle_d 23.9
c_mcbond_it 1.3
c_bond_d 0.007
c_scangle_it 2.91
c_mcangle_it 2.25
c_improper_angle_d 0.88
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Sigma A (Observed) 0.49
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14608
Nucleic Acid Atoms 0
Heterogen Atoms 128
Solvent Atoms 229

Software

Software
Software Name Purpose
HKL-2000 data collection
MOLREP phasing
CNS refinement version: 1.1
HKL-2000 data reduction
SCALEPACK data scaling