X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.1 M MMT buffer, 25% PEG 1500, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.53 α = 90
b = 51.48 β = 90
c = 73.35 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 MARMOSAIC 300 mm CCD MIRROR 2013-01-30
Diffraction Radiation
Monochromator Protocol
SI-111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G

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
1.3 30 99.8 0.065 -- -- 6.7 42130 42130 -- -3.0 --
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)
1.3 1.32 97.9 0.52 -- 2.5 3.8 --

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 1.3 29.89 -- -- 39942 39942 2127 99.77 -- 0.12631 0.12434 0.16349 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 1.3 1.334 -- 155 2850 0.219 0.265 -- 98.11
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.819
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 11.395
r_sphericity_free 35.811
r_rigid_bond_restr 4.95
r_scbond_it 4.116
r_mcangle_it 2.312
r_mcbond_other 1.982
r_mcbond_it 1.998
r_gen_planes_other 0.002
r_gen_planes_refined 0.01
r_chiral_restr 0.13
r_dihedral_angle_4_deg 15.808
r_dihedral_angle_3_deg 9.642
r_dihedral_angle_2_deg 36.239
r_dihedral_angle_1_deg 4.949
r_angle_other_deg 0.868
r_angle_refined_deg 1.884
r_bond_other_d 0.001
r_bond_refined_d 0.017
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1412
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 312

Software

Computing
Computing Package Purpose
Blu Max Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0032 refinement
PHENIX model building
Blu version: Max data collection