X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details PEG 4000, 100 mM NH4Cl, 100 mM TrisCl pH 8.0, 5mM azaserine

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.16 α = 90
b = 60.02 β = 100.42
c = 74.78 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 -- 2016-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.97872 ESRF BM14

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
1.97 73.55 97.9 -- -- -- 6.0 -- 35250 -- -- --
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)
2.0 2.07 85.5 -- -- 2.21 4.7 --

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 1.97 42.12 -- -- -- 33530 1706 96.63 -- 0.14587 0.14342 0.19401 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 1.973 2.025 -- 78 1737 0.218 0.236 -- 68.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.288
Anisotropic B[1][1] 2.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.6
Anisotropic B[2][2] -2.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.59
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.679
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 13.875
r_scangle_other 3.581
r_dihedral_angle_2_deg 37.114
r_gen_planes_refined 0.007
r_angle_refined_deg 1.524
r_mcangle_other 2.378
r_long_range_B_other 4.997
r_angle_other_deg 1.394
r_scbond_other 2.375
r_bond_refined_d 0.008
r_chiral_restr 0.076
r_bond_other_d 0.001
r_mcangle_it 2.378
r_dihedral_angle_1_deg 7.089
r_long_range_B_refined 5.044
r_mcbond_other 1.679
r_dihedral_angle_4_deg 12.801
r_scbond_it 2.375
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4153
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 434

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0232
HKL-2000 data collection version: 9.9.8.9
HKL-2000 data reduction version: 9.9.8.9
HKL-2000 data scaling version: 9.9.8.9
PHASER phasing version: 9.9.8.9
Coot model building version: 0.8.3