X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
Temperature 295.0
Details Tris.HCl, MgCl2, EDTA, sodium monothiophosphate, ATP NaCl, spermidine, PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.77 α = 90
b = 155.29 β = 90
c = 271.02 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2014-11-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2

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
3.3 46.31 97.3 0.232 -- -- 3.4 -- 67483 -- -- --
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)
3.3 3.38 99.1 0.681 -- 1.5 3.5 4574

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 3.3 46.31 -- 0.0 -- 63612 3354 95.72 -- 0.2403 0.2386 0.2747 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 3.3 3.386 -- 232 4640 0.35 0.368 -- 95.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 78.365
Anisotropic B[1][1] -2.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 11.657
r_angle_refined_deg 0.891
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 4.099
r_chiral_restr 0.056
r_bond_refined_d 0.005
r_mcangle_it 2.206
r_scbond_it 1.056
r_dihedral_angle_4_deg 8.694
r_mcbond_it 1.234
r_dihedral_angle_2_deg 31.286
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23993
Nucleic Acid Atoms 0
Heterogen Atoms 175
Solvent Atoms 25

Software

Software
Software Name Purpose
MOSFLM data reduction
Aimless data scaling version: 0.1.29
PHASER phasing
REFMAC refinement version: 5.8.0048
Coot model building version: 0.8.2
PDB_EXTRACT data extraction version: 3.15