X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details 0.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.41 α = 90
b = 100.41 β = 90
c = 384.44 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2017-02-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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
1.85 50 100.0 -- 0.08 -- 18.0 -- 64323 -- -- 22.0
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)
1.85 1.91 99.6 -- 0.65 2.2 14.0 --

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 1.85 50.0 -- -- -- 61142 3058 99.88 -- 0.16601 0.16491 0.18784 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 1.85 1.898 -- 214 4434 0.311 0.35 -- 98.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.271
Anisotropic B[1][1] 0.5
Anisotropic B[1][2] 0.25
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.62
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.552
r_chiral_restr 0.09
r_dihedral_angle_2_deg 34.465
r_long_range_B_other 5.627
r_gen_planes_other 0.001
r_scangle_other 2.696
r_mcbond_it 0.771
r_mcbond_other 0.771
r_dihedral_angle_1_deg 6.172
r_bond_refined_d 0.012
r_mcangle_it 1.29
r_scbond_other 1.552
r_dihedral_angle_3_deg 14.297
r_gen_planes_refined 0.006
r_mcangle_other 1.29
r_angle_other_deg 0.959
r_long_range_B_refined 6.145
r_angle_refined_deg 1.557
r_dihedral_angle_4_deg 19.257
r_bond_other_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3870
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 478

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
HKL-2000 data processing version: 712
HKL-2000 data scaling version: 712
PHASER phasing version: 2.5.6