Experiment: 1Q23

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PD5	Isomorphous structure of the apoenzyme form of CAT I pdbID 1PD5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	290	methanol,calcium chloride,mes,sodium fusidate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.354	α = 90
b = 129.198	β = 108.3
c = 118.073	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	MARRESEARCH	BENT MIRROR	2002-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.811	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.18	6.7	97.9	0.059	0.059	9.8	3.5	182115	182115	2	2	32.34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.18	2.23	99.4		0.286	0.234	3.6	3.3	25486

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Isomorphous structure of the apoenzyme form of CAT I pdbID 1PD5	2.18	111.8	161964	8603	99.74	0.19512	0.1915	0.26324	RANDOM	33.344

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]
5.28		2.04	-2.11		-1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.022
r_scangle_it	5.714
r_scbond_it	4.125
r_angle_refined_deg	2.963
r_mcangle_it	2.542
r_mcbond_it	1.495
r_chiral_restr	0.364
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.221
r_symmetry_hbond_refined	0.188

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.022
r_scangle_it	5.714
r_scbond_it	4.125
r_angle_refined_deg	2.963
r_mcangle_it	2.542
r_mcbond_it	1.495
r_chiral_restr	0.364
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.221
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.185
r_bond_refined_d	0.036
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21253
Nucleic Acid Atoms
Solvent Atoms	582
Heterogen Atoms	445

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	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.