2IQF | pdb_00002iqf

Crystal structure of Helicobacter pylori catalase compound I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QWL	PDB entry 1QWL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	15% PEG MME550, 0.1M Sodium citrate, 10mM ZnSO4, 3mM Sodium azide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.385	α = 90
b = 154.286	β = 90
c = 95.808	γ = 90

Symmetry
Space Group	P 21 21 2

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 4		2003-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.97950	ESRF	ID14-1

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	1.86	37	97.4	0.084	6.4	4.1	80997	74135		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)
	1.86	1.95	97.4		0.4	1.5	3.7	11375

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 (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 1QWL	1.86	37	74135	3928	96.4	0.15051	0.14847	0.16	0.18845	0.19	RANDOM	13.633

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]
0.64			-0.32		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.846
r_dihedral_angle_4_deg	18.539
r_dihedral_angle_3_deg	14.184
r_dihedral_angle_1_deg	6.302
r_scangle_it	2.625
r_scbond_it	1.931
r_angle_refined_deg	1.555
r_angle_other_deg	1.394
r_mcangle_it	1.153
r_mcbond_it	1.007
r_symmetry_vdw_other	0.251
r_mcbond_other	0.209
r_nbd_refined	0.206
r_nbd_other	0.203
r_symmetry_hbond_refined	0.19
r_symmetry_vdw_refined	0.186
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.108
r_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8135
Nucleic Acid Atoms
Solvent Atoms	884
Heterogen Atoms	92

Software

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