X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 298.0
Details MyabA.00309.a.A1.PS01029 at 53.09 mg/mL,0.1M Bis-Tris HCl pH 5.5, 200mM NaCl, 25% PEG3350, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.95 α = 90
b = 107.33 β = 90
c = 137.1 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2012-09-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
1.8 50 98.4 0.079 -- -- -- -- 54053 -- -3.0 --
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)
1.8 1.85 93.7 0.471 -- 3.45 -- --

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 1.8 46.87 -- -- -- 51307 2746 98.42 -- 0.16744 0.16607 0.19363 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 1.8 1.847 -- 182 3600 0.204 0.222 -- 93.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.646
Anisotropic B[1][1] -0.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 14.785
r_bond_refined_d 0.008
r_dihedral_angle_2_deg 30.098
r_angle_other_deg 0.775
r_dihedral_angle_3_deg 11.933
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.183
r_chiral_restr 0.074
r_angle_refined_deg 1.302
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3039
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 547

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.1
REFMAC refinement version: 5.7.0029
PDB_EXTRACT data extraction version: 3.11
XDS data reduction