X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 290.0
Details 0.2 M CaCl2, 0.1 M HEPES, 20% PEG6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.64 α = 90
b = 72.92 β = 109.6
c = 57.56 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD beryllium lenses 2016-11-30
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.14 30 92.2 0.06 -- -- 4.4 -- 144464 -- -- --
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)
1.14 1.16 90.6 0.57 -- 2.1 4.0 --

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 1.14 30.0 -- -- -- 137008 7428 92.09 -- 0.13059 0.12911 0.15785 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 1.141 1.171 -- 540 9794 0.224 0.225 -- 89.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.867
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.16
Anisotropic B[2][2] -0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.86
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_free 20.89
r_angle_refined_deg 2.002
r_angle_other_deg 1.116
r_dihedral_angle_2_deg 35.651
r_chiral_restr 0.289
r_scbond_other 2.569
r_long_range_B_refined 4.021
r_dihedral_angle_1_deg 6.442
r_bond_other_d 0.002
r_mcbond_it 1.299
r_mcangle_it 1.607
r_sphericity_bonded 10.485
r_dihedral_angle_4_deg 17.648
r_bond_refined_d 0.02
r_scbond_it 2.573
r_gen_planes_other 0.002
r_long_range_B_other 3.932
r_dihedral_angle_3_deg 11.997
r_rigid_bond_restr 4.966
r_mcbond_other 1.296
r_scangle_other 2.86
r_mcangle_other 1.607
r_gen_planes_refined 0.01
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3463
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 682

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing