X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 289.0
Details 0.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.54 α = 90
b = 128.54 β = 90
c = 125.94 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r MIRRORS 2012-11-08
Diffraction Radiation
Monochromator Protocol
Si(111) channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM

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
2.1 50 100.0 0.062 -- -- 11.2 -- 68701 0.0 -3.0 26.1
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)
2.1 2.14 100.0 0.819 -- 3.5 10.6 3403

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 2.1 39.94 -- 0.0 -- 67856 3427 98.66 -- 0.1692 0.1679 0.1925 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 2.1 2.154 -- 224 3993 0.21 0.248 -- 83.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.3943
Anisotropic B[1][1] -0.43
Anisotropic B[1][2] -0.43
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.03
r_dihedral_angle_2_deg 32.52
r_dihedral_angle_4_deg 14.55
r_bond_refined_d 0.009
r_bond_other_d 0.004
r_chiral_restr 0.072
r_dihedral_angle_3_deg 13.193
r_dihedral_angle_1_deg 5.396
r_gen_planes_refined 0.005
r_gen_planes_other 0.003
r_angle_refined_deg 1.448
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7016
Nucleic Acid Atoms 0
Heterogen Atoms 192
Solvent Atoms 495

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
SBC-Collect data collection
HKL-3000 data reduction
HKL-3000 data scaling
BALBES phasing