X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 293.0
Details 30.00% polyethylene glycol 3000, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.81 α = 90
b = 51.07 β = 90
c = 52.44 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-19
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 -- ALS 8.2.2

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
1.38 39.81 99.8 0.045 -- -- 7.0 -- 22613 -- -3.0 16.745
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)
1.38 1.43 99.6 0.841 -- 1.5 -- --

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
SAD 1.38 39.81 -- 0.0 -- 22564 1152 99.89 -- 0.1509 0.1494 0.1795 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 1.38 1.416 -- 66 1556 0.253 0.292 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.1093
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.23
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.468
r_sphericity_free 7.608
r_rigid_bond_restr 1.912
r_scangle_it 6.592
r_scbond_it 4.694
r_mcangle_it 4.03
r_mcbond_other 1.851
r_bond_refined_d 0.013
r_bond_other_d 0.002
r_angle_refined_deg 1.567
r_angle_other_deg 1.025
r_dihedral_angle_1_deg 6.041
r_dihedral_angle_2_deg 41.573
r_dihedral_angle_3_deg 13.045
r_dihedral_angle_4_deg 16.273
r_chiral_restr 0.103
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 2.601
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 910
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 154

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.5.0110 refinement
Xscale version: March 15, 2012 data processing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation