6Q10

Crystal structure of the soluble domain (residues 71-217) of a conserved hypothetical secreted protein (Rv2700 ortholog) from Mycobacterium marinum


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 290.0
Details Hampton Research Index screen, condition H1 (305884h1): 100mM Citric acid pH 3.5, 2000mM Ammonium sulfate: MymaA.19257.a.B3.PS38530 at 22.5mg/ml cryo: 25% EG: tray 305841 H1: puck bqx9-4. For experimental phasing, a crystal from the same condition, Index H1 (305884h1), was soaked for 15 seconds each in a mix of 87.5% reservoir / 12.5% 2.5M sodium iodide in ethylene glycol, followed by a soak in 75% reservoir / 25% 2.5M sodium iodide in ethylene glycol, vitrified in liquid nitrogen for in-house data collection at Cu-Kalpha wavelength: puck vgz4-3

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.31 α = 90
b = 46.57 β = 90
c = 69.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2019-04-18
CCD RAYONIX MX-300 -- 2019-04-11
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
RIGAKU VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
1.6 38.7 99.1 0.029 -- -- 6.683 -- 18638 -- -- 31.596
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)
1.6 1.64 91.8 0.348 -- 3.45 4.344 --

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
SAD 1.6 38.7 -- 1.36 -- 18589 1866 99.11 -- 0.1731 0.17 0.2033 0
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 1.6001 1.6433 -- 142 1172 0.2286 0.2634 0.0 92.0
X Ray Diffraction 1.6433 1.6917 -- 133 1245 0.2115 0.2694 0.0 98.0
X Ray Diffraction 1.6917 1.7463 -- 153 1263 0.1901 0.2512 0.0 100.0
X Ray Diffraction 1.7463 1.8087 -- 122 1284 0.1838 0.1939 0.0 100.0
X Ray Diffraction 1.8087 1.8811 -- 140 1291 0.1815 0.2279 0.0 100.0
X Ray Diffraction 1.8811 1.9667 -- 160 1264 0.1697 0.1862 0.0 100.0
X Ray Diffraction 1.9667 2.0704 -- 149 1265 0.1684 0.2071 0.0 100.0
X Ray Diffraction 2.0704 2.2001 -- 138 1298 0.1694 0.212 0.0 100.0
X Ray Diffraction 2.2001 2.3699 -- 131 1312 0.1739 0.1921 0.0 100.0
X Ray Diffraction 2.3699 2.6084 -- 154 1294 0.1734 0.2024 0.0 100.0
X Ray Diffraction 2.6084 2.9857 -- 154 1294 0.1817 0.2174 0.0 100.0
X Ray Diffraction 2.9857 3.7612 -- 130 1346 0.1655 0.1831 0.0 100.0
X Ray Diffraction 3.7612 38.7 -- 160 1395 0.1561 0.1975 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.2634
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_plane_restr 0.007
f_dihedral_angle_d 9.71
f_chiral_restr 0.063
f_angle_d 1.027
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1058
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 125

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement version: dev_3500
PDB_EXTRACT data extraction version: 3.25
PHASER phasing
PARROT phasing
ARP/wARP model building