X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Temperature 293.0
Details 25 MG ML-1 YIHQ PROTEIN STOCK IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.1-0.15 M CACL2, AND BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 DEGREE. THE LIGAND I5F WAS SOAKED INTO THE NATIVE CRYSTAL.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.67 α = 90
b = 112.64 β = 109.52
c = 111.88 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2015-04-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 -- Diamond I04

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 49.68 98.6 0.05 -- -- 4.0 -- 154198 -- -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)
1.85 1.88 95.7 0.62 -- 2.1 3.7 --

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 1.85 105.45 -- -- -- 146377 7578 98.35 -- 0.16189 0.16026 0.19337 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 -- 555 10430 0.318 0.327 -- 94.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.762
Anisotropic B[1][1] -1.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.91
Anisotropic B[2][2] -2.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.72
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_dihedral_angle_2_deg 35.12
r_dihedral_angle_3_deg 14.556
r_bond_refined_d 0.02
r_mcbond_other 3.229
r_angle_refined_deg 1.858
r_scbond_it 3.986
r_mcbond_it 3.231
r_angle_other_deg 1.077
r_dihedral_angle_1_deg 7.259
r_gen_planes_refined 0.01
r_bond_other_d 0.003
r_chiral_restr 0.13
r_dihedral_angle_4_deg 17.534
r_mcangle_it 4.164
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10757
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 724

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0095
MOLREP phasing