2HVW

Crystal structure of dCMP deaminase from Streptococcus mutans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HVV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES, PH6.5, 12% Dioxane, 1.6M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.262

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.498α = 90
b = 99.657β = 90
c = 141.388γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.661692.90.06610.19.8796737401711
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)
1.661.7268.60.4677.25412

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HVV1.67167967374010372294.210.1510.150.1490.179RANDOM20.322
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]
-0.180.57-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg13.643
r_dihedral_angle_3_deg11.8
r_dihedral_angle_1_deg5.595
r_scangle_it2.138
r_angle_refined_deg1.616
r_scbond_it1.469
r_mcangle_it0.892
r_mcbond_it0.572
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg13.643
r_dihedral_angle_3_deg11.8
r_dihedral_angle_1_deg5.595
r_scangle_it2.138
r_angle_refined_deg1.616
r_scbond_it1.469
r_mcangle_it0.892
r_mcbond_it0.572
r_nbtor_refined0.301
r_nbd_refined0.208
r_symmetry_vdw_refined0.206
r_symmetry_hbond_refined0.186
r_chiral_restr0.168
r_xyhbond_nbd_refined0.146
r_metal_ion_refined0.018
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3520
Nucleic Acid Atoms
Solvent Atoms784
Heterogen Atoms171

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling