5B6E

Crystal Structure of cytidine monophosphate hydroxymethylase MilA with hmCMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JNH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.52890.1 M sodium cacodylate trihydrate(pH 6.5), 1.4 M sodium acetate trihydrate
Crystal Properties
Matthews coefficientSolvent content
2.6753.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.323α = 90
b = 109.323β = 90
c = 112.867γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97912SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85010019.611.268810
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.86

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 REPLACEMENTTHROUGHOUT5JNH1.849.2468810351599.880.18810.18720.2075RANDOM22.571
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]
-0.1-0.1-0.10.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.368
r_dihedral_angle_4_deg13.717
r_dihedral_angle_3_deg11.636
r_dihedral_angle_1_deg5.085
r_mcangle_it1.036
r_angle_refined_deg0.984
r_angle_other_deg0.698
r_mcbond_it0.603
r_mcbond_other0.603
r_chiral_restr0.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.368
r_dihedral_angle_4_deg13.717
r_dihedral_angle_3_deg11.636
r_dihedral_angle_1_deg5.085
r_mcangle_it1.036
r_angle_refined_deg0.984
r_angle_other_deg0.698
r_mcbond_it0.603
r_mcbond_other0.603
r_chiral_restr0.055
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5089
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHASERphasing