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_dihedral_angle_3_deg 9.642
r_bond_refined_d 0.017
r_mcbond_other 1.982
r_scbond_it 4.116
r_dihedral_angle_4_deg 15.808
r_dihedral_angle_1_deg 4.949
r_bond_other_d 0.001
r_mcangle_it 2.312
r_angle_refined_deg 1.884
r_gen_planes_other 0.002
r_angle_other_deg 0.868
r_chiral_restr 0.13
r_dihedral_angle_2_deg 36.239
r_mcbond_it 1.998
r_sphericity_free 35.811
r_sphericity_bonded 11.395
r_gen_planes_refined 0.01
r_rigid_bond_restr 4.95
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

Software
Software Name Purpose
Blu data collection version: Max
PHENIX model building
REFMAC refinement version: 5.7.0032
XDS data reduction
XDS data scaling
PHENIX phasing