X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 298.0
Details Drop composition: 25 mM Tris, 2.5% glycerol, 75 mM KCl, 1-5% PEG MME 550, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.8 α = 90
b = 88.43 β = 90
c = 52.5 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 1.0720 APS 24-ID-C

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
1.9 50 97.5 0.049 -- -- 9.1 63056 33586 -- -- --
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)
1.9 1.97 85.4 0.492 -- 2.4 8.8 --

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 1.9 45.15 -- -- -- 30366 1576 95.18 -- 0.22205 0.2203 0.25605 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 1.9 1.948 -- 84 1625 0.295 0.325 -- 83.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.652
Anisotropic B[1][1] 3.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.24
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.28
r_dihedral_angle_2_deg 37.176
r_angle_refined_deg 1.327
r_dihedral_angle_4_deg 20.694
r_chiral_restr 0.11
r_dihedral_angle_1_deg 6.974
r_scangle_it 5.017
r_mcangle_it 2.12
r_gen_planes_refined 0.012
r_dihedral_angle_3_deg 17.077
r_scbond_it 3.439
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2780
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 146

Software

Software
Software Name Purpose
CBASS data collection
PHASER phasing
REFMAC refinement version: 5.5.0088
HKL-2000 data reduction
HKL-2000 data scaling