X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 0.1 M BIS-TRIS pH 5.5 (5.5-7.5), 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.1 α = 90
b = 76.1 β = 90
c = 130.95 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2011-07-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.0000 SSRL BL9-2

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
1.8 50 99.9 -- 0.05 -- 3.5 -- n/a -- -- 30.0
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)
1.8 1.86 99.8 -- 0.458 2.6 3.4 7872

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 1.8 50.0 -- -- -- 74552 3948 99.84 -- 0.16988 0.16855 0.19444 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 1.8 1.847 -- 289 5548 0.292 0.337 -- 99.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.952
Anisotropic B[1][1] 1.11
Anisotropic B[1][2] 0.56
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.67
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.789
r_scbond_it 3.945
r_mcangle_it 2.446
r_mcbond_it 1.554
r_gen_planes_refined 0.007
r_chiral_restr 0.099
r_dihedral_angle_4_deg 18.169
r_dihedral_angle_3_deg 12.047
r_dihedral_angle_2_deg 32.996
r_dihedral_angle_1_deg 5.977
r_angle_refined_deg 1.395
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4894
Nucleic Acid Atoms 0
Heterogen Atoms 127
Solvent Atoms 555

Software

Computing
Computing Package Purpose
Blue-ice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHASES model building
Blue-ice data collection