X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 7 mg/ml of protein in 50 mM Hepes buffer (pH 7.5) with 150 mM NaCl, mixesd with 1:1 ratio with 18% (w/v) PEG 3350, 0.2 M amonium formate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 165.7 α = 90
b = 53.8 β = 114.72
c = 87.39 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300HE -- 2016-05-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID

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
2.1 99 98.6 0.077 -- 27.43 9.4 -- 40748 -- -- --
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)
2.1 2.18 89.7 0.634 -- -- 8.0 --

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 2.1 79.38 -- 0.0 -- 30056 1080 75.47 -- 0.1707 0.1687 0.2304 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 2.099 2.154 -- 26 598 0.19 0.248 -- 20.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.996
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1
Anisotropic B[2][2] 0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 8.552
r_chiral_restr 0.108
r_mcbond_other 8.508
r_bond_refined_d 0.018
r_angle_other_deg 1.067
r_bond_other_d 0.004
r_dihedral_angle_3_deg 16.306
r_angle_refined_deg 1.852
r_dihedral_angle_4_deg 15.98
r_mcangle_it 10.503
r_dihedral_angle_2_deg 33.718
r_dihedral_angle_1_deg 6.908
r_gen_planes_refined 0.024
r_gen_planes_other 0.018
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4036
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 185

Software

Software
Software Name Purpose
SERGUI data collection
SCALEPACK data scaling
PHASER phasing version: 2.1.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.20
HKL-3000 data reduction