7BZ1

The mutant variant of PNGM-1. H96 was substituted for alanine to study metal coordination.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6J4N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.42870.1 M Sodium acetate, 1.5 M Sodium formate, 0.08 M CaCl2 and 10% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3146.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.638α = 90
b = 82.545β = 110.77
c = 163.716γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.97940PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.445090.80.1240.1390.066.45.150546
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.592.60.4140.4630.2020.8975

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6j4n2.4548.0848014248589.990.18980.18620.2596RANDOM28.766
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.908
r_dihedral_angle_4_deg17.773
r_dihedral_angle_3_deg17.507
r_dihedral_angle_1_deg8.617
r_angle_refined_deg1.654
r_angle_other_deg1.268
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.908
r_dihedral_angle_4_deg17.773
r_dihedral_angle_3_deg17.507
r_dihedral_angle_1_deg8.617
r_angle_refined_deg1.654
r_angle_other_deg1.268
r_chiral_restr0.07
r_bond_refined_d0.009
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 Atoms11537
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing