X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details 0.7 M Ammonium sulfate 25.5 % (w/v) PEG 4000, 15 % (v/v) Glycerol, 5 mM zinc acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.76 α = 90
b = 50.86 β = 106.98
c = 70.72 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 315r mirrors 2011-04-15
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97918 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
2.35 50 97.6 0.144 -- -- 3.8 16892 16892 0.0 0.0 24.97
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)
2.35 2.39 80.9 0.448 -- 2.0 2.2 709

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 2.35 40.65 -- 0.0 16745 16745 842 97.55 0.212 0.212 0.208 0.283 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 2.35 2.4972 2445 124 2321 0.2899 0.4055 -- 86.0
X Ray Diffraction 2.4972 2.69 2857 137 2704 0.228 0.3131 -- 100.0
X Ray Diffraction 2.69 2.9606 2818 136 2682 0.2061 0.3166 -- 100.0
X Ray Diffraction 2.9606 3.3889 2864 167 2697 0.1965 0.2976 -- 100.0
X Ray Diffraction 3.3889 4.2689 2857 150 2707 0.1715 0.2416 -- 100.0
X Ray Diffraction 4.2689 40.6561 2920 128 2792 0.2167 0.2486 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 30.6
Anisotropic B[1][1] -0.8486
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 10.8873
Anisotropic B[2][2] -7.2363
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.0849
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.011
f_chiral_restr 0.125
f_dihedral_angle_d 16.859
f_angle_d 1.615
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3369
Nucleic Acid Atoms 0
Heterogen Atoms 70
Solvent Atoms 170

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection