X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.3
Temperature 298.0
Details 1.8M sodium malonate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.27 α = 90
b = 123.27 β = 90
c = 123.27 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2009-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1

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
2.3 50 99.5 0.058 -- -- 6.4 27974 27835 1.0 -- --
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)
2.3 2.38 97.0 0.758 -- 1.9 4.6 2742

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 2.3 30.0 -- -- -- 26386 1410 99.29 -- 0.15256 0.15041 0.19325 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 2.3 2.36 -- 96 1854 0.446 0.436 -- 95.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.4
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 9.043
r_scbond_it 6.307
r_mcangle_it 3.93
r_mcbond_it 2.389
r_gen_planes_refined 0.005
r_chiral_restr 0.066
r_dihedral_angle_4_deg 21.823
r_dihedral_angle_3_deg 17.034
r_dihedral_angle_2_deg 38.06
r_dihedral_angle_1_deg 5.258
r_angle_refined_deg 1.127
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2866
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 82

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
REFMAC Structure Solution
REFMAC 5.5.0088 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0088 refinement
REFMAC model building
HKL-2000 data collection