6UDG

Crystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 290.0
Details Anatrace Morpheus screen, well g8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium Ltartrate, sodium oxamate: 100mM MOPS/HEPES-Na pH 7.5: ElanA.00055.a.B1, PW38308, at 23mg/ml: cryo: direct: tray 294018 g8: puck xoe2-6.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.59 α = 90
b = 107.8 β = 90
c = 113.7 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-300 -- 2017-11-24
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.65 48.7 99.7 0.07 -- -- 4.84 -- 19753 -- -- 64.797
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)
2.65 2.72 99.8 0.618 -- 2.84 4.983 --

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 2.65 48.7 -- 1.35 -- 19723 2096 99.58 -- 0.2171 0.2095 0.2805 --
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 2.65 2.71 -- 151 1151 0.354 0.4076 0.0 100.0
X Ray Diffraction 2.71 2.78 -- 146 1120 0.3262 0.4365 0.0 100.0
X Ray Diffraction 2.78 2.85 -- 150 1165 0.3142 0.4275 0.0 100.0
X Ray Diffraction 2.85 2.94 -- 118 1161 0.2914 0.3831 0.0 100.0
X Ray Diffraction 2.94 3.03 -- 140 1151 0.2855 0.4115 0.0 99.0
X Ray Diffraction 3.03 3.14 -- 135 1167 0.2703 0.4183 0.0 100.0
X Ray Diffraction 3.14 3.27 -- 139 1154 0.2651 0.3199 0.0 100.0
X Ray Diffraction 3.27 3.42 -- 102 1203 0.242 0.3319 0.0 100.0
X Ray Diffraction 3.42 3.6 -- 132 1193 0.2083 0.3063 0.0 100.0
X Ray Diffraction 3.6 3.82 -- 155 1153 0.201 0.2568 0.0 100.0
X Ray Diffraction 3.82 4.12 -- 116 1200 0.1956 0.3276 0.0 100.0
X Ray Diffraction 4.12 4.53 -- 170 1142 0.168 0.2253 0.0 99.0
X Ray Diffraction 4.53 5.19 -- 138 1197 0.1608 0.2366 0.0 100.0
X Ray Diffraction 5.19 6.53 -- 156 1197 0.2094 0.2285 0.0 100.0
X Ray Diffraction 6.53 48.7 -- 148 1273 0.1686 0.2253 0.0 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 80.7365
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.449
f_plane_restr 0.006
f_angle_d 0.733
f_bond_d 0.004
f_chiral_restr 0.048
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4546
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 11

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.25
MoRDa phasing
PHENIX model building
Coot model building