X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 24% PEG 3350, 0.250 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-176, pH 7.5, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.32 α = 90
b = 72.62 β = 103.9
c = 67.36 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 DECTRIS PILATUS 6M -- 2010-12-10
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.97945 SSRL BL12-2

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
1.95 39.4 97.6 -- 0.068 -- 4.2 32294 32294 -- -- --
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)
1.95 2.05 93.0 0.673 0.673 1.1 4.0 4466

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 1.95 37.23 -- 0.0 -- 32270 1664 97.32 -- 0.1985 0.1965 0.2341 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 1.948 1.998 -- 108 1963 0.34 0.376 -- 86.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.7158
Anisotropic B[1][1] 0.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.74
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.07
r_dihedral_angle_4_deg 17.719
r_dihedral_angle_3_deg 14.338
r_dihedral_angle_2_deg 36.93
r_dihedral_angle_1_deg 5.088
r_angle_other_deg 0.844
r_angle_refined_deg 1.205
r_bond_other_d 0.001
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3654
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 76

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SCALA version: 3.3.16 data reduction