3NJJ | pdb_00003njj

P115A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N55

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	0.1 M Bis-Tris buffer, 0.3 M magnesium formate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.104	α = 90
b = 100.104	β = 90
c = 101.086	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	SBC-3		2005-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9792	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.56	28.9	99.1	0.046	10.8	10	27489	27489			33.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.59	90.6		0.656	2.03	6.1	1448

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3N55	1.56	28.9	27165	27165	2083	97.93	0.157	0.157	0.154	0.18	0.181	0.2	RANDOM	13.53

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]
0.02	0.01		0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.897
r_dihedral_angle_4_deg	42.484
r_dihedral_angle_3_deg	12.022
r_dihedral_angle_1_deg	6.24
r_scangle_it	5.77
r_scbond_it	3.833
r_mcangle_it	2.708
r_mcbond_it	1.795
r_angle_refined_deg	1.653
r_rigid_bond_restr	1.618

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.897
r_dihedral_angle_4_deg	42.484
r_dihedral_angle_3_deg	12.022
r_dihedral_angle_1_deg	6.24
r_scangle_it	5.77
r_scbond_it	3.833
r_mcangle_it	2.708
r_mcbond_it	1.795
r_angle_refined_deg	1.653
r_rigid_bond_restr	1.618
r_angle_other_deg	0.945
r_mcbond_other	0.583
r_chiral_restr	0.116
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	887
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.