X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.9
Temperature 298.0
Details 12% PEG4000, 0.1M NaCl, 0.1M NaAc, 0.2M NH4Ac, 0.001M DTT, 0.02% DDM, Tris/HCl, 0.0003M NQNO (a menaquinone analog), pH 5.9, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126 α = 90
b = 165.3 β = 90
c = 212.8 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
PIXEL PSI PILATUS 6M -- 2012-06-29
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97908 ESRF ID29

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
3.2 49.12 97.8 0.08 -- -- -- 73321 138472 0.0 -3.0 89.561
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)
3.2 3.3 97.1 1.054 -- 1.16 -- --

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 3.3 25.0 -- 0.0 67491 66832 3298 99.27 0.2018 0.2018 0.1999 0.236 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 3.3 3.384 4592 229 4592 0.344 0.348 -- 99.24
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS + isotropic (possible thanks to tight ncs restraints)
Mean Isotropic B 105.957
Anisotropic B[1][1] 7.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.834
r_scbond_it 2.306
r_mcangle_it 1.661
r_mcbond_it 0.837
r_gen_planes_refined 0.005
r_chiral_restr 0.082
r_dihedral_angle_4_deg 15.385
r_dihedral_angle_3_deg 17.099
r_dihedral_angle_2_deg 35.949
r_dihedral_angle_1_deg 5.28
r_angle_refined_deg 1.161
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 30002
Nucleic Acid Atoms 0
Heterogen Atoms 316
Solvent Atoms 40

Software

Computing
Computing Package Purpose
MXCuBE Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser molecular replacement
Xscale data reduction