1SXY

1.07 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus


X-RAY DIFFRACTION

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
1.9537.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.142α = 90
b = 42.776β = 94.05
c = 52.979γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Bent cylindrical Si-mirror (Rh coating)2002-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.900APS14-BM-D

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
11.0719.8397.60.0560.05624.25.3767346673465.48
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)
1.071.1196.80.2010.2019.15.226648

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 1D2U1.0719.86734663529338696.920.150690.150690.149550.17199RANDOM8.156
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]
-0.19-0.030.10.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.896
r_sphericity_free4.895
r_scangle_it3.562
r_sphericity_bonded3.381
r_scbond_it2.501
r_mcangle_it2.155
r_angle_other_deg1.927
r_angle_refined_deg1.759
r_mcbond_it1.461
r_rigid_bond_restr1.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.896
r_sphericity_free4.895
r_scangle_it3.562
r_sphericity_bonded3.381
r_scbond_it2.501
r_mcangle_it2.155
r_angle_other_deg1.927
r_angle_refined_deg1.759
r_mcbond_it1.461
r_rigid_bond_restr1.343
r_symmetry_vdw_other0.262
r_nbd_other0.252
r_nbd_refined0.222
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.176
r_chiral_restr0.108
r_symmetry_hbond_refined0.104
r_nbtor_other0.088
r_metal_ion_refined0.016
r_bond_refined_d0.014
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 Atoms1473
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDISPLAYFdata reduction
d*TREKdata scaling