X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 25 mM MES pH6.5 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.77 α = 90
b = 87.08 β = 90.04
c = 79.68 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-10-12
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID

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 30 94.2 0.079 -- -- 3.9 37378 35327 0.0 0.0 --
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)
2.3 2.38 98.6 0.294 -- -- 4.0 3693

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 2.31 29.39 -- 0.0 37523 35266 1754 93.53 0.1876 0.1876 0.1855 0.228 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 2.31 2.38 -- 144 2629 0.2032 0.2664 -- 93.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.631
Anisotropic B[1][1] 2.8937
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.2817
Anisotropic B[2][2] -12.4557
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.562
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 17.92
t_omega_torsion 3.41
t_angle_deg 1.07
t_bond_d 0.009
t_ideal_dist_contact 0.0
t_chiral_improper_torsion 0.0
t_it 0.0
t_gen_planes 0.0
t_trig_c_planes 0.0
t_dihedral_angle_d 0.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.305
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6326
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 289

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
BUSTER 2.10.0 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
BUSTER-TNT refinement
Phaser version: 2.3.0 molecular replacement
SCALEPACK data reduction