X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 290.0
Details 23 mg/mL RifeA.00170.a.B1.PS01660, MCSG1 screen condition G1: 10% PEG8000, 8% ethylene glycol, 100 mM HEPES/NaOH, pH 7.5, Tray 241460g1, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.11 α = 90
b = 99.7 β = 90
c = 73.37 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Rh coated flat mirror 2012-02-18
Diffraction Radiation
Monochromator Protocol
Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1

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
2 50 99.8 0.042 -- -- 4.83 38963 38871 0.0 -3.0 38.1
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)
2.0 2.05 100.0 0.523 -- 3.37 -- --

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 2.0 46.95 -- 0.0 38963 38831 1949 99.77 0.1751 0.1751 0.1733 0.2103 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 2.0 2.052 -- 140 2676 0.236 0.288 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC, TLS
Mean Isotropic B 39.9812
Anisotropic B[1][1] -0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.605
r_mcbond_other 1.658
r_bond_refined_d 0.015
r_bond_other_d 0.004
r_angle_refined_deg 1.296
r_angle_other_deg 0.859
r_dihedral_angle_1_deg 5.903
r_dihedral_angle_2_deg 34.785
r_dihedral_angle_3_deg 12.766
r_dihedral_angle_4_deg 17.068
r_chiral_restr 0.083
r_gen_planes_refined 0.008
r_gen_planes_other 0.004
r_mcbond_it 1.658
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3478
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 266

Software

Computing
Computing Package Purpose
BluIce Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0032 refinement
Phaser version: 2.5.2 molecular replacement
Xscale data reduction