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_mcbond_other 1.658
r_mcbond_it 1.658
r_bond_refined_d 0.015
r_chiral_restr 0.083
r_mcangle_it 2.605
r_angle_refined_deg 1.296
r_angle_other_deg 0.859
r_dihedral_angle_4_deg 17.068
r_dihedral_angle_2_deg 34.785
r_dihedral_angle_1_deg 5.903
r_bond_other_d 0.004
r_gen_planes_other 0.004
r_gen_planes_refined 0.008
r_dihedral_angle_3_deg 12.766
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

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.2
REFMAC refinement version: 5.7.0032
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection