3RGS

Structural and kinetic analysis of the beef liver catalase with the ammonia as a ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BLC	PDB entry 4BLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	45-60mM Mg Formate mixed with 12-13 mg/ml protein containing 1-5 wt% of NH4OH, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.48	α = 90
b = 140.72	β = 90
c = 229.52	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator	2009-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	1.987	57.38	100	0.094	0.094	9.8	5.7	172258	172258			14.2

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)
1	1.99	2.03	91.5		0.303	0.303	2.5	5.5	54827

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 4BLC	1.99	57.38	171515	171515	8405	92.4	0.161	0.161	0.161	0.198	RANDOM	18.7

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]
2.64			-3.91		1.27

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.1
c_scangle_it	2.61
c_scbond_it	1.89
c_mcangle_it	1.61
c_angle_deg	1.3
c_mcbond_it	1.11
c_improper_angle_d	0.92
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16068
Nucleic Acid Atoms
Solvent Atoms	2266
Heterogen Atoms	176

Software

Software
Software Name	Purpose
HKL-3000	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	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.