9AZH | pdb_00009azh

Native nnhA in P1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9AZG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2293Protein at 7mg/mL was set up in SD2 sitting drop plates with 300 nL protein and 150 nL reservoir at 20 C. Reservoir consisted of 21% polyacrylic acid 5100, 20 mM MgCl2 and 100 mM HEPES at pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.8456.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.727α = 117.139
b = 117.377β = 91.298
c = 121.125γ = 101.377
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.18157Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.0460.7498.20.2220.090.9879.67177958
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.0794.60.8430.390.6962.25.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.0454.09177656860198.020.1570.15590.16760.17850.189713.886
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]
1.884-0.515-0.166-0.726-0.338-0.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.716
r_dihedral_angle_3_deg11.742
r_dihedral_angle_2_deg9.724
r_dihedral_angle_1_deg6.412
r_lrange_it5.258
r_lrange_other5.258
r_scangle_it3.718
r_scangle_other3.718
r_scbond_it2.336
r_scbond_other2.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.716
r_dihedral_angle_3_deg11.742
r_dihedral_angle_2_deg9.724
r_dihedral_angle_1_deg6.412
r_lrange_it5.258
r_lrange_other5.258
r_scangle_it3.718
r_scangle_other3.718
r_scbond_it2.336
r_scbond_other2.336
r_mcangle_it1.92
r_mcangle_other1.92
r_angle_refined_deg1.546
r_mcbond_it1.253
r_mcbond_other1.252
r_angle_other_deg0.531
r_nbd_refined0.208
r_nbd_other0.193
r_symmetry_nbd_other0.183
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_refined0.169
r_xyhbond_nbd_refined0.156
r_symmetry_nbd_refined0.155
r_symmetry_xyhbond_nbd_other0.103
r_chiral_restr0.077
r_symmetry_nbtor_other0.076
r_ncsr_local_group_50.056
r_ncsr_local_group_10.055
r_ncsr_local_group_30.052
r_ncsr_local_group_40.052
r_ncsr_local_group_120.05
r_ncsr_local_group_20.049
r_ncsr_local_group_60.048
r_ncsr_local_group_110.046
r_ncsr_local_group_100.045
r_ncsr_local_group_70.043
r_ncsr_local_group_90.042
r_ncsr_local_group_150.042
r_ncsr_local_group_140.041
r_ncsr_local_group_80.038
r_ncsr_local_group_130.038
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17346
Nucleic Acid Atoms
Solvent Atoms1733
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing