X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 289.0
Details 0.1M bis-tris propane, 0.9M DL-malic acid, 0.005M zinc chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 179.66 α = 90
b = 113.75 β = 109.33
c = 175.71 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r MIRROR 2012-11-11
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97857 APS 19-ID

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
2.2 50 94.9 0.069 -- -- 2.1 -- 169402 -- -3.0 39.7
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)
2.2 2.24 96.1 0.41 -- -- 2.0 8494

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 2.2 36.71 -- 0.0 -- 160372 8016 94.79 -- 0.1731 0.1715 0.2046 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 2.2 2.257 -- 583 11399 0.242 0.276 -- 96.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.6984
Anisotropic B[1][1] 0.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.01
Anisotropic B[2][2] -1.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.22
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.007
r_gen_planes_refined 0.006
r_chiral_restr 0.076
r_dihedral_angle_4_deg 16.29
r_dihedral_angle_3_deg 13.913
r_dihedral_angle_2_deg 35.093
r_dihedral_angle_1_deg 5.649
r_angle_other_deg 3.62
r_angle_refined_deg 1.335
r_bond_other_d 0.0
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19400
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 1183

Software

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