1OC3 | pdb_00001oc3

HUMAN PEROXIREDOXIN 5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HD2	PDB ENTRY 1HD2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.3		PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.1 M SODIUM CITRATE BUFFER, PH 5.3, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE

Crystal Properties
Matthews coefficient	Solvent content
2.89	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.195	α = 90
b = 102.053	β = 90
c = 145.06	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	MARRESEARCH	PREMIRROR, BENT MIRROR	2002-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	2	40	96.9	0.047	13.5	4.2		38821

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	2	2.2	96.1		0.332	3.4	4

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 1HD2	2	72.55	36850	1933	96.8	0.223	0.221	0.26	0.259	0.3	RANDOM	22.93

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]
4.8			-1.21		-3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.816
r_dihedral_angle_1_deg	4.963
r_scangle_it	4.504
r_scbond_it	2.739
r_angle_refined_deg	1.945
r_mcangle_it	1.554
r_mcbond_it	0.913
r_angle_other_deg	0.901
r_symmetry_vdw_refined	0.397
r_symmetry_vdw_other	0.245
r_nbd_refined	0.235
r_symmetry_hbond_refined	0.227
r_nbd_other	0.216
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.118
r_xyhbond_nbd_other	0.096
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3576
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing