X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 6% PEG 20000, 100 mM MES pH 6.5, 2.0 mM RM-1-176 in 10% DMSO, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.17 α = 78.73
b = 63.48 β = 88.48
c = 74 γ = 89.93
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M -- 2010-12-09
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 0.9795 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
2.65 52.6 81.0 -- 0.195 -- 3.8 17677 17677 -- -- --
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)
2.65 2.79 72.9 0.01 1.011 0.7 3.7 2313

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 2.65 72.55 -- 0.0 -- 17677 866 80.85 -- 0.2102 0.2081 0.2518 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 2.65 2.719 -- 75 1172 0.38 0.376 -- 78.23
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.6264
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.56
Anisotropic B[1][3] -0.8
Anisotropic B[2][2] -1.17
Anisotropic B[2][3] 1.11
Anisotropic B[3][3] 0.73
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.003
r_gen_planes_refined 0.005
r_chiral_restr 0.066
r_dihedral_angle_4_deg 14.461
r_dihedral_angle_3_deg 15.207
r_dihedral_angle_2_deg 36.648
r_dihedral_angle_1_deg 5.96
r_angle_other_deg 0.983
r_angle_refined_deg 1.304
r_bond_other_d 0.003
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4173
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 13

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
MOSFLM 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: 3.3.20 data reduction