3MPZ

Crystal structure of CYTIDINE DEAMINASE from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IJFpdb entry 3ijf

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290MD PACT SCREEN E9; 20% PEG 3350, 200MM NA/K TARTRATE; protein at 40MG/ML, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.8433.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.28α = 90
b = 96.11β = 90
c = 178.19γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.75098.20.04322.0145170850775-320.35
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)
11.71.7485.10.2713.21.93219

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 REPLACEMENTTHROUGHOUTpdb entry 3ijf1.7505170850615257097.90.1580.1580.1560.192RANDOM11.7
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]
-0.050.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.512
r_dihedral_angle_4_deg16.442
r_dihedral_angle_3_deg14.112
r_dihedral_angle_1_deg5.178
r_scangle_it3.612
r_scbond_it2.255
r_mcangle_it1.558
r_angle_refined_deg1.436
r_angle_other_deg1.047
r_mcbond_it0.884
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.512
r_dihedral_angle_4_deg16.442
r_dihedral_angle_3_deg14.112
r_dihedral_angle_1_deg5.178
r_scangle_it3.612
r_scbond_it2.255
r_mcangle_it1.558
r_angle_refined_deg1.436
r_angle_other_deg1.047
r_mcbond_it0.884
r_mcbond_other0.219
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3520
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms4

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling