3RGP | pdb_00003rgp

Structural and Kinetic Analysis of the Beef liver Catalase complexed with Nitric Oxide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	1. 45-60mM Mg Formate mixed with 12-13 mg/ml protein containing 1-5 wt% of NH4OH. 2. Crystals then soaked overnight in 80 mM Mg-Formate solution, pH 6.7, 3. Finally soaked in 80 mM Mg formate and 150 mM bis-tris & 10-100mM DEANO, pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.11	α = 90
b = 139.94	β = 90
c = 228.02	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	2009-07-17	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	1.88	40.301	100	0.091	0.091	11.5	5.1	205859	205959			16.1

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	1.88	1.92	89.9		0.329	0.091	2.1	5.1	64188

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry code 4BLC	1.88	40.3	205859	205859	10125	92	0.18	0.18	0.18	0.18	0.214	0.18	RANDOM	22.8

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]
-3.43			-2.87		6.3

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.2
c_scangle_it	2.69
c_mcangle_it	2.37
c_scbond_it	1.93
c_mcbond_it	1.75
c_angle_deg	1.3
c_improper_angle_d	0.96
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16068
Nucleic Acid Atoms
Solvent Atoms	2020
Heterogen Atoms	180

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.