1DJ9 | pdb_00001dj9

CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
1	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.89	α = 90
b = 58.89	β = 90
c = 201.77	γ = 120

Symmetry
Space Group	P 31 1 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	IMAGE PLATE	MARRESEARCH		1998-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX7.2		SRS	PX7.2

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	1.99	31.62	99.3	0.065	6.3	2.9	28007	27822			37

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	1.99	2.06	93.5		0.452		2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO	FREE R	2	10	27177	27314	820	99.5	0.212	0.212	0.212	0.278	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		3208

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.1
s_zero_chiral_vol	0.03
s_non_zero_chiral_vol	0.03
s_from_restr_planes	0.025
s_angle_d	0.02
s_bond_d	0.007
s_similar_dist
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2912
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	39

Software

Software
Software Name	Purpose
X-PLOR	model building
SHELXL-97	refinement
MAR345	data collection
SCALEPACK	data scaling
X-PLOR	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.