2HJR

Crystal Structure of Cryptosporidium parvum malate dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GUY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629815% PEG4K, 0.2M NH4oAC, Nacitrate pH 5.6, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7455.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 171.887α = 90
b = 171.887β = 90
c = 135.606γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.22099.90.1170.07514.65227472227351
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2899.90.8640.7371.9114.722734

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GUY2.219.832156271139199.960.200480.200480.197990.24747RANDOM34.344
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.965
r_dihedral_angle_4_deg25.429
r_dihedral_angle_3_deg17.785
r_dihedral_angle_1_deg5.29
r_scangle_it2.839
r_scbond_it1.817
r_angle_refined_deg1.516
r_mcangle_it1.085
r_mcbond_it0.628
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.965
r_dihedral_angle_4_deg25.429
r_dihedral_angle_3_deg17.785
r_dihedral_angle_1_deg5.29
r_scangle_it2.839
r_scbond_it1.817
r_angle_refined_deg1.516
r_mcangle_it1.085
r_mcbond_it0.628
r_nbtor_refined0.3
r_symmetry_vdw_refined0.234
r_nbd_refined0.214
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.159
r_chiral_restr0.125
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28040
Nucleic Acid Atoms
Solvent Atoms1337
Heterogen Atoms588

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing