1SY2

1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Ammonium Phosphate 2.8 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9637.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.149α = 90
b = 42.804β = 93.93
c = 52.881γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Flat mirror (vertical focusing)2002-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1

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
10.9921.498.80.0490.04927.34.6285962859626.62
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)
0.991.0399.40.1570.1577.73.348609

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 1D2U121.48596277984410497.270.15630.15630.155590.1696RANDOM8.691
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]
-0.07-0.030.050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.532
r_sphericity_free3.625
r_scangle_it3.165
r_sphericity_bonded2.915
r_scbond_it2.155
r_mcangle_it1.987
r_angle_refined_deg1.66
r_mcbond_it1.29
r_rigid_bond_restr1.09
r_angle_other_deg0.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.532
r_sphericity_free3.625
r_scangle_it3.165
r_sphericity_bonded2.915
r_scbond_it2.155
r_mcangle_it1.987
r_angle_refined_deg1.66
r_mcbond_it1.29
r_rigid_bond_restr1.09
r_angle_other_deg0.794
r_nbd_other0.254
r_symmetry_vdw_other0.219
r_nbd_refined0.217
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.117
r_nbtor_other0.11
r_chiral_restr0.098
r_symmetry_hbond_refined0.058
r_bond_refined_d0.012
r_metal_ion_refined0.009
r_gen_planes_refined0.008
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 Atoms1450
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
d*TREKdata scaling