1SY0

1.15 A Crystal Structure of T121V Mutant of Nitrophorin 4 from Rhodnius Prolixus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D2UPDB entry 1D2U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9537.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.3α = 90
b = 42.763β = 93.66
c = 52.89γ = 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
11.1521.3797.10.050.0520.83.1954132541325.78
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)
1.151.1998.60.1340.13462.515460

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 1D2U1.1521.375413250570272795.620.14280.14280.141280.17179RANDOM8.884
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]
-0.02-0.12-0.220.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.836
r_sphericity_free5.273
r_scangle_it3.648
r_sphericity_bonded3.241
r_scbond_it2.612
r_mcangle_it2.347
r_angle_other_deg1.868
r_angle_refined_deg1.829
r_mcbond_it1.531
r_rigid_bond_restr1.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.836
r_sphericity_free5.273
r_scangle_it3.648
r_sphericity_bonded3.241
r_scbond_it2.612
r_mcangle_it2.347
r_angle_other_deg1.868
r_angle_refined_deg1.829
r_mcbond_it1.531
r_rigid_bond_restr1.473
r_nbd_refined0.346
r_nbd_other0.253
r_symmetry_vdw_other0.242
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.122
r_chiral_restr0.116
r_symmetry_hbond_refined0.089
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1475
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDISPLAYFdata reduction
d*TREKdata scaling