X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details MyabA.00937.a.A1 PW30232 at 24.4 mg/mL against JCSG + E1, 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5 with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 219633e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.66 α = 90
b = 79.08 β = 90
c = 86.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-02-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1

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
1.7 50 98.5 0.045 -- -- 6.5 55952 55136 -- -3.0 27.064
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)
1.7 1.74 97.6 0.495 -- 3.78 6.6 4112

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 1.7 50.0 -- 0.0 -- 54992 2798 98.29 -- 0.1723 0.1709 0.1975 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 1.7 1.744 -- 202 3794 0.232 0.281 -- 97.27
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.637
Anisotropic B[1][1] -0.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.76
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 17.194
r_scbond_it 2.419
r_bond_refined_d 0.014
r_dihedral_angle_3_deg 12.437
r_dihedral_angle_2_deg 32.659
r_dihedral_angle_1_deg 5.433
r_gen_planes_refined 0.009
r_scangle_it 3.976
r_chiral_restr 0.101
r_angle_refined_deg 1.448
r_mcbond_it 0.912
r_mcangle_it 1.629
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3352
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 390

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
BOS data collection
XDS data reduction