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_bond_refined_d 0.008
r_gen_planes_refined 0.004
r_bond_other_d 0.003
r_dihedral_angle_1_deg 5.649
r_dihedral_angle_4_deg 11.318
r_angle_other_deg 0.958
r_gen_planes_other 0.002
r_dihedral_angle_2_deg 36.784
r_dihedral_angle_3_deg 13.62
r_chiral_restr 0.065
r_angle_refined_deg 1.194
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
REFMAC5 refinement
pdb_extract version: 3.10 data extraction