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 9% PEG 4000, 100 mM MES pH 6.5, 5 mM Sodium Acetate, 2.0 mM RM-1-89 in 10% DMSO, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.79 α = 79.32
b = 63.24 β = 89.35
c = 73.3 γ = 89.88
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2011-01-20
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 BL9-2 0.97945 SSRL BL9-2

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
2.27 41.79 96.8 0.101 -- -- 3.9 32963 32963 -- -- 37.7

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 2.27 36.32 -- 0.0 -- 32963 1672 96.77 -- 0.2275 0.226 0.2557 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 2.271 2.33 -- 112 2326 0.338 0.343 -- 95.31
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.2225
Anisotropic B[1][1] 0.39
Anisotropic B[1][2] 0.21
Anisotropic B[1][3] 0.3
Anisotropic B[2][2] -0.69
Anisotropic B[2][3] 0.55
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_gen_planes_refined 0.004
r_chiral_restr 0.065
r_dihedral_angle_4_deg 11.318
r_dihedral_angle_3_deg 13.62
r_dihedral_angle_2_deg 36.784
r_dihedral_angle_1_deg 5.649
r_angle_other_deg 0.958
r_angle_refined_deg 1.194
r_bond_other_d 0.003
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4050
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 69

Software

Computing
Computing Package Purpose
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