X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 294.0
Details 10% PEG 3000, 0.2 M Zn acetate and 0.1 M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.02 α = 90
b = 109.02 β = 90
c = 109.02 γ = 90
Symmetry
Space Group I 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-05-19
Diffraction Radiation
Monochromator Protocol
Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.98 SSRL BL7-1

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
2.05 54.51 99.7 0.148 -- -- 7.4 -- 13751 -- -- --

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 2.05 34.475 -- 1.35 -- 13748 1381 99.58 -- 0.1982 0.1955 0.2234 --
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 2.05 2.1181 -- 136 1213 0.1853 0.2129 -- 99.0
X Ray Diffraction 2.1181 2.2029 -- 141 1245 0.1921 0.2182 -- 100.0
X Ray Diffraction 2.2029 2.3031 -- 136 1227 0.2007 0.2441 -- 100.0
X Ray Diffraction 2.3031 2.4245 -- 137 1229 0.2124 0.2601 -- 100.0
X Ray Diffraction 2.4245 2.5764 -- 135 1209 0.2126 0.2831 -- 100.0
X Ray Diffraction 2.5764 2.7752 -- 141 1248 0.2262 0.2671 -- 1.01
X Ray Diffraction 2.7752 3.0543 -- 129 1224 0.2115 0.2324 -- 100.0
X Ray Diffraction 3.0543 3.4959 -- 143 1259 0.1982 0.2138 -- 100.0
X Ray Diffraction 3.4959 4.4031 -- 144 1248 0.1706 0.2179 -- 100.0
X Ray Diffraction 4.4031 34.48 -- 139 1265 0.1897 0.1856 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.067
f_dihedral_angle_d 16.5
f_angle_d 1.244
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 950
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 99

Software

Computing
Computing Package Purpose
Web-ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
phenix.automr Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
phenix.automr model building
Web-ice data collection