2IW4

CRYSTAL STRUCTURE OF BASILLUS SUBTILIS FAMILY II INORGANIC PYROPHOSPHATASE MUTANT, H98Q, IN COMPLEX WITH PNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WPMPDB ENTRY 1WPM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100MM HEPES/K (PH 7.5) 2.3-2.5M AMMONIUM SULPHATE 3-4% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.7867.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.908α = 90
b = 115.249β = 90
c = 148.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV IMAGE PLATEMIRRORS2003-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
12.153098.90.09153.750598-3
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)
12.152.1997.90.43.33.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1WPM2.153050598255494.20.170.1690.205RANDOM33.79
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]
-0.390.69-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.729
r_dihedral_angle_3_deg15.922
r_dihedral_angle_4_deg12.034
r_dihedral_angle_1_deg5.976
r_scangle_it3.458
r_scbond_it2.159
r_angle_refined_deg1.472
r_mcangle_it1.161
r_mcbond_it0.711
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.729
r_dihedral_angle_3_deg15.922
r_dihedral_angle_4_deg12.034
r_dihedral_angle_1_deg5.976
r_scangle_it3.458
r_scbond_it2.159
r_angle_refined_deg1.472
r_mcangle_it1.161
r_mcbond_it0.711
r_nbtor_refined0.311
r_nbd_refined0.175
r_xyhbond_nbd_refined0.128
r_symmetry_vdw_refined0.122
r_symmetry_hbond_refined0.111
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms486
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing