X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details MyabA.01507.a.A1 PW30392 at 29.54 mg/mL against Wizard III/IV screen condition G8, 2.1 M DL Malic acid, pH 7.0 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220029g8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.8 α = 90
b = 156.92 β = 90
c = 57.76 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 -- 2011-03-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 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
2.3 50 97.4 0.147 -- -- 5.5 40352 39296 -- -3.0 24.91
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)
2.3 2.36 93.1 0.527 -- 3.19 4.8 2719

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 2.3 50.0 -- 0.0 -- 39144 1950 97.01 -- 0.1624 0.1601 0.207 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 2.3 2.36 -- 129 2577 0.186 0.245 -- 92.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.2985
Anisotropic B[1][1] -1.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.94
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.557
r_angle_refined_deg 1.38
r_dihedral_angle_3_deg 13.514
r_dihedral_angle_4_deg 18.183
r_scangle_it 2.744
r_chiral_restr 0.09
r_mcangle_it 0.835
r_gen_planes_refined 0.007
r_scbond_it 1.707
r_mcbond_it 0.471
r_bond_refined_d 0.013
r_dihedral_angle_2_deg 37.474
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6761
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 538

Software

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