3ZUK

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN COMPLEX WITH INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DMTPDB ENTRY 1DMT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG MME 2000
Crystal Properties
Matthews coefficientSolvent content
2.754.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.29α = 90
b = 198.77β = 90
c = 63.27γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.630950.112.23.64822240.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.7475.60.372.62.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DMT2.6304607093892.770.176610.175090.24964RANDOM30.02
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]
-0.16-0.280.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.958
r_dihedral_angle_4_deg18.967
r_dihedral_angle_3_deg17.195
r_dihedral_angle_1_deg5.706
r_scangle_it3.178
r_scbond_it1.95
r_angle_refined_deg1.516
r_mcangle_it1.157
r_mcbond_it0.603
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.958
r_dihedral_angle_4_deg18.967
r_dihedral_angle_3_deg17.195
r_dihedral_angle_1_deg5.706
r_scangle_it3.178
r_scbond_it1.95
r_angle_refined_deg1.516
r_mcangle_it1.157
r_mcbond_it0.603
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10374
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms514

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing