2O4H | pdb_00002o4h

Human brain aspartoacylase complex with intermediate analog (N-phosphonomethyl-L-aspartate)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I3C	PDB entry 2I3C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	8-10 mg/ml Protein, 50 mM Sodium citrate pH 6.0, 300 mM K2HPO4, 15-19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.74	67.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.081	α = 90
b = 143.081	β = 90
c = 104.604	γ = 90

Symmetry
Space Group	P 42 21 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	MARMOSAIC 300 mm CCD	Kirkpatrick-Baez pair of focusing bimorph mirrors	2006-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.28300	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.7	50	95.3	0.094	20.7	10.7	28991	27490			72.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	62.7		0.354	2.9	5.3	1849

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2I3C	2.7	46.47	27490	27490	1449	95.23	0.20544	0.20211	0.19	0.27138	0.25	RANDOM	59.981

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]
0.58			0.58		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.018
r_dihedral_angle_3_deg	19.608
r_dihedral_angle_4_deg	10.473
r_dihedral_angle_1_deg	7.269
r_scangle_it	2.779
r_angle_refined_deg	1.639
r_scbond_it	1.639
r_mcangle_it	1.346
r_mcbond_it	0.748
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.018
r_dihedral_angle_3_deg	19.608
r_dihedral_angle_4_deg	10.473
r_dihedral_angle_1_deg	7.269
r_scangle_it	2.779
r_angle_refined_deg	1.639
r_scbond_it	1.639
r_mcangle_it	1.346
r_mcbond_it	0.748
r_nbtor_refined	0.318
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.099
r_symmetry_hbond_refined	0.067
r_metal_ion_refined	0.042
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4842
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	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.