2AT3

1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X8OPDB entry 1X8O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6300ammonium phosphate, imidazole, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal Properties
Matthews coefficientSolvent content
1.5319.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.221α = 90
b = 42.743β = 94.09
c = 52.886γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateFlat mirror (vertical focusing)2002-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.751SSRLBL9-1

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
1119.8197.40.040.0420.83.238194710
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)
11.048888.10.250.252.61.527330

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 SYNTHESISFREE RPDB entry 1X8O119.818193781937414597.390.1450.1450.1440.167RANDOM8.376
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]
0.13-0.160.13-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.95
r_dihedral_angle_3_deg13.355
r_dihedral_angle_4_deg7.792
r_dihedral_angle_1_deg7.381
r_sphericity_free7.035
r_sphericity_bonded3.532
r_scangle_it3.187
r_scbond_it2.584
r_mcangle_it1.896
r_angle_refined_deg1.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.95
r_dihedral_angle_3_deg13.355
r_dihedral_angle_4_deg7.792
r_dihedral_angle_1_deg7.381
r_sphericity_free7.035
r_sphericity_bonded3.532
r_scangle_it3.187
r_scbond_it2.584
r_mcangle_it1.896
r_angle_refined_deg1.658
r_rigid_bond_restr1.596
r_mcbond_it1.541
r_mcbond_other1.031
r_angle_other_deg0.889
r_nbd_refined0.489
r_nbd_other0.235
r_symmetry_vdw_other0.211
r_nbtor_refined0.186
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.148
r_chiral_restr0.095
r_nbtor_other0.088
r_metal_ion_refined0.014
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1798
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms48

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
CrystalCleardata scaling