6Q10

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP290Hampton 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 Properties
Matthew coefficientSolvent content
2.141.5

Crystal Data

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

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002019-04-11MSINGLE WAVELENGTH
21x-ray100CCDRIGAKU SATURN 944+2019-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F
2ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.638.799.10.0290.031131.676.6831863831.596
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6491.80.3480.3950.9013.454.344

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.638.71.3618589186699.110.17310.170.2033031.2634
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.71
f_angle_d1.027
f_chiral_restr0.063
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1058
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building