X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.8
Temperature 318.0
Details 50mM sodium acetate, 1-1.5M NaCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 318K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.47 α = 90
b = 92.35 β = 90
c = 114.24 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
IMAGE PLATE MAR scanner 345 mm plate Mirrors 2011-12-09
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
2.65 50 92.9 0.188 -- -- 3.4 10188 10188 2.0 2.0 28.9
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)
2.67 2.72 82.9 0.515 -- 2.0 2.0 391

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 2.654 35.909 2.0 0.0 9436 9436 451 92.34 -- 0.2076 0.2031 0.2996 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 2.6539 3.0378 -- 144 2602 0.2625 0.3746 -- 83.0
X Ray Diffraction 3.0378 3.8266 -- 158 3130 0.1894 0.2824 -- 98.0
X Ray Diffraction 3.8266 35.9124 -- 149 3253 0.1917 0.2796 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 28.9
Anisotropic B[1][1] -1.4881
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4725
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.9606
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.086
f_dihedral_angle_d 14.492
f_angle_d 1.257
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3003
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 69

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
PHASES model building
HKL-2000 data collection