X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.2
Temperature 293.0
Details 0.2 M NaCl, 0.1 M Ph-Citrate pH4.2, 20% PEG8K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.45 α = 90
b = 90.43 β = 103.75
c = 44.13 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
PIXEL DECTRIS EIGER X 9M -- 2016-08-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.07822 APS 21-ID-D

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 50 97.7 0.062 0.062 29.1 6.3 -- 70520 0.0 -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 1.31 99.3 0.876 0.876 1.9 4.5 --

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 1.3 45.22 -- -- -- 62288 3179 91.17 -- 0.12553 0.12375 0.16073 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 -- 110 2385 0.246 0.276 -- 46.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.613
Anisotropic B[1][1] 0.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 1.42
r_gen_planes_other 0.002
r_bond_other_d 0.002
r_gen_planes_refined 0.006
r_mcbond_other 1.786
r_long_range_B_other 4.111
r_angle_refined_deg 1.45
r_dihedral_angle_3_deg 11.566
r_mcangle_it 2.28
r_mcbond_it 1.786
r_sphericity_free 28.223
r_scangle_other 4.064
r_chiral_restr 0.087
r_sphericity_bonded 12.366
r_scbond_it 3.256
r_angle_other_deg 0.932
r_dihedral_angle_2_deg 35.881
r_mcangle_other 2.28
r_long_range_B_refined 4.792
r_scbond_other 3.249
r_bond_refined_d 0.012
r_dihedral_angle_4_deg 19.422
r_dihedral_angle_1_deg 6.073
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2420
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 363

Software

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