2HZY | pdb_00002hzy

Mouse fumarylacetoacetate hydrolase complexes with a transition-state mimic of the complete substrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QCN	PDB ENTRY 1QCN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M Sodium cacodylate, 0.3 M Sodium acetate, 30% (w/v) PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.144	α = 90
b = 109.472	β = 102.35
c = 67.491	γ = 90

Symmetry
Space Group	P 1 21 1

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	APS-1	ID-19	2001-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98000	APS	19-ID

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	1.35	30	94.6	0.06	19.9	4.37		188128	0.2		17.8

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)
	1.35	1.4	79.7		0.444	2.6	3.1

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	PDB ENTRY 1QCN	1.35	24.14	188088	188088	9466	94.6	0.16901	0.16901	0.16799	0.17	0.18815	0.19	RANDOM	17.84

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]
-0.66		-0.23	1.41		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.803
r_scangle_it	4.055
r_scbond_it	2.635
r_mcangle_it	1.819
r_angle_refined_deg	1.787
r_mcbond_it	1.057
r_metal_ion_refined	0.341
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.803
r_scangle_it	4.055
r_scbond_it	2.635
r_mcangle_it	1.819
r_angle_refined_deg	1.787
r_mcbond_it	1.057
r_metal_ion_refined	0.341
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.12
r_bond_refined_d	0.022
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6489
Nucleic Acid Atoms
Solvent Atoms	998
Heterogen Atoms	45

Software

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