X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 295.0
Details Protein: 14.6 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (A7), 0.2M Sodium chloride, 0.1M Sodium acetate pH (5.0), 20% (w/v) PEG 6000.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.38 α = 90
b = 111.71 β = 100.42
c = 96.95 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 300 mm CCD C(111) 2017-03-28
Diffraction Radiation
Monochromator Protocol
Be 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
1.36 30 99.1 0.087 0.087 -- 4.3 -- 280381 -- -3.0 10.5
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)
1.36 1.38 96.5 0.715 0.715 2.07 3.7 --

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 1.36 29.62 -- -- -- 266396 13944 98.93 -- 0.14453 0.14333 0.16782 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 1.361 1.396 -- 971 18812 0.232 0.248 -- 94.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.977
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.13
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_other 1.149
r_dihedral_angle_3_deg 9.905
r_bond_refined_d 0.009
r_angle_other_deg 0.867
r_mcangle_other 1.094
r_scangle_other 1.773
r_mcbond_it 0.664
r_mcangle_it 1.094
r_gen_planes_other 0.021
r_mcbond_other 0.664
r_angle_refined_deg 1.446
r_long_range_B_refined 4.605
r_dihedral_angle_2_deg 32.676
r_bond_other_d 0.001
r_scbond_it 1.149
r_long_range_B_other 3.997
r_dihedral_angle_1_deg 3.926
r_chiral_restr 0.093
r_gen_planes_refined 0.024
r_dihedral_angle_4_deg 13.994
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11050
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 2247

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
HKL-3000 data reduction
HKL-3000 data scaling
MOLREP phasing