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, 85 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.06 α = 79.06
b = 63.4 β = 87.72
c = 74.96 γ = 90.08
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 2008-07-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.000000 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
2.6 40 94.0 0.077 -- -- -- 23389 21983 -- -3.0 38.29
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)
2.6 2.7 92.5 0.221 -- 6.2 -- 2324

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 2.6 40.0 -- 0.0 23389 21983 880 100.0 -- 0.213 0.21 0.284 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 2.6 2.667 1543 65 1543 0.372 0.421 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.622
Anisotropic B[1][1] 0.89
Anisotropic B[1][2] -0.34
Anisotropic B[1][3] 0.4
Anisotropic B[2][2] -1.09
Anisotropic B[2][3] 0.19
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.5
r_scbond_it 2.279
r_mcangle_it 1.573
r_mcbond_it 0.927
r_symmetry_hbond_refined 0.16
r_bond_refined_d 0.018
r_angle_refined_deg 1.893
r_dihedral_angle_1_deg 7.443
r_dihedral_angle_2_deg 39.203
r_dihedral_angle_3_deg 20.607
r_dihedral_angle_4_deg 18.744
r_chiral_restr 0.126
r_gen_planes_refined 0.007
r_nbd_refined 0.245
r_nbtor_refined 0.325
r_xyhbond_nbd_refined 0.203
r_symmetry_vdw_refined 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4143
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 53

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE 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: 3.006 data extraction
REFMAC5 refinement
Phaser molecular replacement
Xscale data processing