3NJI | pdb_00003nji

S114A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis.

X-RAY DIFFRACTION

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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	1 M ammonium sulfate, 0.1 M Bis-Tris buffer, 1% PEG-3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.833	α = 90
b = 99.833	β = 90
c = 99.8	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	ADSC QUANTUM 315		2008-03-12	M	SINGLE WAVELENGTH

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

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	1.8	43.2	99.6	0.068	14.1	9.7	17886	17886			42.8

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	1.8	1.83	94.2		0.613	1.97	4.8	824

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	1.8	43.2	17729	17729	907	98.71	0.1674	0.1674	0.1663	0.1776	0.1889	0.1995	RANDOM	41.472

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]
0.43	0.21		0.43		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.423
r_dihedral_angle_4_deg	19.525
r_dihedral_angle_3_deg	16.491
r_dihedral_angle_1_deg	6.523
r_scangle_it	3.831
r_scbond_it	2.374
r_mcangle_it	1.7
r_angle_refined_deg	1.609
r_mcbond_it	1.01
r_angle_other_deg	0.892
r_mcbond_other	0.294
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	955
Nucleic Acid Atoms
Solvent Atoms	104
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
HKL-2000	data scaling
MOLREP	phasing