X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 298.0
Details 0.17M ammonium acetate, 0.085 M sodium citrate-HCl, pH 5.6, 25.5% PEG4000, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.66 α = 90
b = 160.08 β = 90
c = 192.65 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-09-01
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A

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 50 98.3 0.132 -- -- 3.4 -- 180659 -- -- --
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 97.3 0.868 -- -- 3.3 8898

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
SAD 2.0 20.01 -- 0.0 -- 95313 4762 98.75 -- 0.1763 0.1748 0.2056 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 2.002 2.054 -- 346 6506 0.256 0.288 -- 97.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.9759
Anisotropic B[1][1] -1.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.83
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.004
r_gen_planes_refined 0.007
r_chiral_restr 0.075
r_dihedral_angle_4_deg 16.855
r_dihedral_angle_3_deg 13.754
r_dihedral_angle_2_deg 33.284
r_dihedral_angle_1_deg 5.919
r_angle_other_deg 1.034
r_angle_refined_deg 1.248
r_bond_other_d 0.005
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10034
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 877

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-3000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Phenix Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction