1MRL | pdb_00001mrl

Crystal structure of streptogramin A acetyltransferase with dalfopristin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MR7PDB ENTRY 1MR7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2900.2M Sodium Fluoride, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.8656.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.914α = 90
b = 90.905β = 90
c = 104.529γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2002-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.8700SRSPX9.6

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
12.8300.08215.53.72011840
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)
12.82.870.3583.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MR72.81518853100999.770.27230.27230.270630.260.303790.29RANDOM27.92
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]
1.392.27-3.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg14.407
r_dihedral_angle_1_deg2.287
r_angle_refined_deg1.597
r_symmetry_hbond_refined0.433
r_symmetry_vdw_refined0.393
r_nbd_refined0.254
r_xyhbond_nbd_refined0.134
r_chiral_restr0.08
r_gen_planes_refined0.007
r_bond_refined_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg14.407
r_dihedral_angle_1_deg2.287
r_angle_refined_deg1.597
r_symmetry_hbond_refined0.433
r_symmetry_vdw_refined0.393
r_nbd_refined0.254
r_xyhbond_nbd_refined0.134
r_chiral_restr0.08
r_gen_planes_refined0.007
r_bond_refined_d0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4744
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms144

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement