X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 24% PEG 5000, 0.3M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.47 α = 90
b = 59.54 β = 98.6
c = 59.36 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 MAR CCD 165 mm Mirrors 2009-03-09
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 1.033 APS 14-ID-B

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
1.68 50 98.8 -- 0.064 -- 3.8 -- 39171 0.0 2.0 --

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 1.9 40.0 -- -- -- 26425 1412 98.86 -- 0.19905 0.19638 0.24797 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 1.9 1.949 -- 89 1981 0.201 0.24 -- 99.81
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 30.998
Anisotropic B[1][1] -3.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.21
Anisotropic B[2][2] 1.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.18
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.726
r_dihedral_angle_4_deg 16.702
r_dihedral_angle_2_deg 42.266
r_angle_refined_deg 1.534
r_mcbond_it 3.215
r_dihedral_angle_3_deg 13.977
r_dihedral_angle_1_deg 7.358
r_bond_other_d 0.003
r_bond_refined_d 0.008
r_chiral_restr 0.101
r_gen_planes_other 0.001
r_mcangle_it 4.382
r_scbond_it 3.801
r_mcbond_other 3.216
r_gen_planes_refined 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3053
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 83

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
REFMAC refinement version: 5.5.0102
PDB_EXTRACT data extraction version: 3.14
BioCARS-developed data collection version: GUI
HKL-2000 data reduction
HKL-2000 data scaling