1YE9 | pdb_00001ye9

Crystal structure of proteolytically truncated catalase HPII from E. coli

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GGE	PDB Entry 1GGE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	50mM TrisHCl, 8% PEG 20000, 8% PEG MME 550, 0.2M KSCN, 0.1M dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.011	α = 90
b = 152.888	β = 97.54
c = 135.287	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	Mirrors	2003-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	2.8	30	95.4	0.07	0.106	6.6	3.3	109986	104927	3	3

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)
	2.8	2.87	92.1		0.65	1	3	7510

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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 1GGE	2.8	30	3	3	109968	99638	5289	100	0.248	0.21977	0.21713	0.2174	0.26902	0.2649	RANDOM	43.725

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]
1.05		2.66	-2.62		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.411
r_scangle_it	5.019
r_scbond_it	3.184
r_angle_refined_deg	2.048
r_mcangle_it	1.926
r_mcbond_it	1.036
r_symmetry_vdw_refined	0.449
r_symmetry_hbond_refined	0.381
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.202
r_metal_ion_refined	0.173
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31183
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	352

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing