3NJM | pdb_00003njm

P117A 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	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
3.51	64.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.438	α = 90
b = 99.438	β = 90
c = 101.147	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		2005-11-23	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	1.64	28.7	99.9	0.048	8.9	10.4	23667	23667			33

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	1.64	1.67	100		0.816	2.25	9.8	1172

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	1.64	28.7	23401	23401	1210	98.87	0.164	0.164	0.163	0.1794	0.19	0.2114	RANDOM	27.996

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]
-0.16	-0.08		-0.16		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.224
r_dihedral_angle_4_deg	20.748
r_dihedral_angle_3_deg	14.493
r_dihedral_angle_1_deg	6.424
r_scangle_it	4.114
r_scbond_it	2.547
r_mcangle_it	2.037
r_angle_refined_deg	1.845
r_angle_other_deg	1.39
r_mcbond_it	1.208
r_mcbond_other	0.347
r_chiral_restr	0.182
r_bond_refined_d	0.019
r_bond_other_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	917
Nucleic Acid Atoms
Solvent Atoms	156
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