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 10% PEG 20000, 15% glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.02 α = 79.6
b = 63.42 β = 87.89
c = 74.2 γ = 89.98
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Dynamically bendable mirror 2010-05-23
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.003900 SLS X10SA

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
3.1 45 91.8 0.062 -- -- 1.79 13657 12539 -- -3.0 43.513
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)
3.1 3.2 93.7 0.205 -- 4.0 1.84 1245

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 3.1 41.99 -- -- 13657 12538 815 100.0 -- 0.2162 0.2115 0.2832 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 3.1 3.18 -- 62 902 0.316 0.445 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.022
Anisotropic B[1][1] -1.31
Anisotropic B[1][2] -0.72
Anisotropic B[1][3] 0.77
Anisotropic B[2][2] -3.62
Anisotropic B[2][3] 0.96
Anisotropic B[3][3] 4.52
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.864
r_scbond_it 1.139
r_mcangle_it 0.98
r_mcbond_it 0.546
r_symmetry_hbond_refined 0.347
r_bond_refined_d 0.012
r_angle_refined_deg 1.363
r_dihedral_angle_1_deg 6.448
r_dihedral_angle_2_deg 36.99
r_dihedral_angle_3_deg 20.492
r_dihedral_angle_4_deg 20.716
r_chiral_restr 0.086
r_gen_planes_refined 0.004
r_nbd_refined 0.24
r_nbtor_refined 0.319
r_xyhbond_nbd_refined 0.164
r_symmetry_vdw_refined 0.262
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4194
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 0

Software

Computing
Computing Package Purpose
SLS-Software Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
Xscale data reduction