X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 289.0
Details BupsA.00608.a.A1 PW30798 at 30.69 mg/mL against JCSG+ screen condition A6, 0.2 M Li2SO4, 0.1 M phosphate/citrate pH 4.2, 20% PEG 1000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220922a6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.24 α = 90
b = 55.24 β = 90
c = 95.42 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-04-10
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
1.7 50 99.5 0.049 -- -- 6.2 19149 19044 -- -3.0 25.389
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 99.8 0.509 -- 3.76 5.1 1393

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 -- 19018 976 99.12 -- 0.2081 0.2064 0.2395 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 -- 87 1299 0.255 0.333 -- 99.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.9592
Anisotropic B[1][1] -0.81
Anisotropic B[1][2] -0.41
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.22
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.399
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.133
r_scangle_it 3.921
r_angle_refined_deg 1.486
r_dihedral_angle_2_deg 36.372
r_mcbond_it 0.794
r_bond_refined_d 0.015
r_dihedral_angle_4_deg 13.979
r_dihedral_angle_3_deg 12.393
r_scbond_it 2.415
r_chiral_restr 0.102
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1261
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 127

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