1U17

1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NP1PDB Entry 2NP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.1 M potassium cacodylate pH 5.3, 2.9 M di-ammoium hydrogen phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2545.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.006α = 90
b = 73.987β = 99.16
c = 65.224γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2003-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.08SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.73099.50.0748.13.94008220.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7498.50.3313.7

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 REPLACEMENTTHROUGHOUTPDB Entry 2NP11.73036923194596.540.184690.184690.181910.23713RANDOM24.646
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]
-0.2-1.60.27-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.3
r_scangle_it5.248
r_scbond_it3.324
r_mcangle_it2.334
r_angle_refined_deg1.962
r_mcbond_it1.313
r_nbd_refined0.227
r_symmetry_hbond_refined0.214
r_chiral_restr0.173
r_symmetry_vdw_refined0.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.3
r_scangle_it5.248
r_scbond_it3.324
r_mcangle_it2.334
r_angle_refined_deg1.962
r_mcbond_it1.313
r_nbd_refined0.227
r_symmetry_hbond_refined0.214
r_chiral_restr0.173
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.16
r_metal_ion_refined0.066
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing