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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.06 α = 78.7
b = 63.69 β = 87.02
c = 75.12 γ = 89.96
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 2008-09-02
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.004730 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 98.2 0.066 -- -- -- 23507 23074 -- -3.0 39.548
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 97.4 0.27 -- 5.7 -- 2506

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 23507 23072 923 100.0 -- 0.223 0.221 0.277 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 1624 67 1624 0.304 0.404 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.864
Anisotropic B[1][1] 0.66
Anisotropic B[1][2] -0.59
Anisotropic B[1][3] 0.2
Anisotropic B[2][2] -0.91
Anisotropic B[2][3] 0.24
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.31
r_scbond_it 2.135
r_mcangle_it 1.455
r_mcbond_it 0.866
r_symmetry_hbond_refined 0.192
r_bond_refined_d 0.019
r_angle_refined_deg 1.865
r_dihedral_angle_1_deg 7.202
r_dihedral_angle_2_deg 39.853
r_dihedral_angle_3_deg 19.159
r_dihedral_angle_4_deg 19.02
r_chiral_restr 0.122
r_gen_planes_refined 0.007
r_nbd_refined 0.243
r_nbtor_refined 0.321
r_xyhbond_nbd_refined 0.211
r_symmetry_vdw_refined 0.289
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4159
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 73

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