X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details PEG4000, LiSO4, DTT, DMM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.71 α = 90
b = 97.4 β = 90
c = 183.73 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
CCD ADSC QUANTUM 315r Toroidal mirror 2011-09-05
Diffraction Radiation
Monochromator Protocol
Silicon (1 1 1) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.00407 ESRF ID23-1

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
1.47 29.57 99.0 0.069 -- -- 2.647 547509 283897 0.0 -3.0 16.861
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)
1.47 1.5 98.9 0.373 -- 2.79 -- --

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 1.47 25.0 0.0 0.0 283873 283873 14104 99.84 0.1243 0.1243 0.1224 0.16 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 1.47 1.508 19677 1082 19677 0.164 0.217 -- 99.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.7922
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 2.204
r_bond_refined_d 0.01
r_angle_refined_deg 1.223
r_dihedral_angle_1_deg 5.619
r_dihedral_angle_2_deg 35.24
r_dihedral_angle_3_deg 11.887
r_dihedral_angle_4_deg 15.264
r_chiral_restr 0.085
r_gen_planes_refined 0.007
r_mcbond_it 2.029
r_mcangle_it 2.87
r_scbond_it 4.162
r_scangle_it 5.671
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13182
Nucleic Acid Atoms 0
Heterogen Atoms 132
Solvent Atoms 1606

Software

Computing
Computing Package Purpose
MXCuBE Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
REFMAC 5.5.0109 Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Xscale data reduction