X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details MymaA.01530.f.A1 PS00846 at 33.15 mg/mL against JCSG+ A5, 0.2 M magnesium formate, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218651a5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.78 α = 90
b = 77.71 β = 107.94
c = 76.47 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-12-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 -- 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
2.2 50 96.9 0.08 -- -- 3.7 36052 34932 -- -3.0 30.815
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)
2.2 2.26 82.0 0.412 -- 2.83 3.3 2672

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 2.2 50.0 -- 0.0 -- 34879 1735 96.86 -- 0.1768 0.1736 0.237 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 2.2 2.257 -- 93 2089 0.226 0.322 -- 81.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.579
Anisotropic B[1][1] 1.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.2
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.98
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 30.33
r_scbond_it 2.072
r_mcangle_it 1.181
r_dihedral_angle_1_deg 5.675
r_dihedral_angle_4_deg 20.629
r_gen_planes_refined 0.006
r_scangle_it 3.505
r_angle_refined_deg 1.441
r_dihedral_angle_3_deg 13.698
r_mcbond_it 0.652
r_bond_refined_d 0.015
r_chiral_restr 0.092
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5332
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 398

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