1SY3

1.00 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Nitric Oxide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KOIPDB entry 1KOI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9637.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.431α = 90
b = 42.729β = 94.27
c = 53.124γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Bent conical Si-mirror (Rh coating)2002-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.900APS14-BM-C

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
1110.6950.0730.07317.25.1285604856043.398
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)
11.0299.10.1240.1243.53.068863

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1KOI19.688560475616400593.850.142810.142810.141930.15924RANDOM7.253
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]
0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.389
r_sphericity_free3.724
r_scangle_it3.019
r_sphericity_bonded2.937
r_scbond_it2.134
r_angle_other_deg2.1
r_mcangle_it2
r_angle_refined_deg1.699
r_mcbond_it1.327
r_rigid_bond_restr1.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.389
r_sphericity_free3.724
r_scangle_it3.019
r_sphericity_bonded2.937
r_scbond_it2.134
r_angle_other_deg2.1
r_mcangle_it2
r_angle_refined_deg1.699
r_mcbond_it1.327
r_rigid_bond_restr1.098
r_nbd_other0.256
r_nbd_refined0.226
r_symmetry_vdw_other0.223
r_metal_ion_refined0.216
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.13
r_xyhbond_nbd_refined0.119
r_chiral_restr0.103
r_nbtor_other0.088
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1535
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDISPLAYFdata reduction
d*TREKdata scaling