2NQX | pdb_00002nqx

Crystal Structure of bovine lactoperoxidase with iodide ions at 2.9A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IPS

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.53	α = 90
b = 80.549	β = 103.74
c = 78.031	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	290	IMAGE PLATE	MAR scanner 345 mm plate	mirror	2006-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.9	25	98.6	0.17	6.5		13026	13026			38.9

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	2.9	3	97.1		0.406	2.1

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2IPS	2.95	25	13026	13026	681	98.5	0.198	0.19603	0.2363	RANDOM	25.324

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]
0.1		-0.91	-0.73		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.057
r_dihedral_angle_3_deg	16.57
r_dihedral_angle_4_deg	14.941
r_dihedral_angle_1_deg	4.233
r_mcangle_it	3.046
r_mcbond_it	2.122
r_scangle_it	1.726
r_angle_refined_deg	1.212
r_scbond_it	1.024
r_symmetry_hbond_refined	0.412
r_nbtor_refined	0.314
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.141
r_symmetry_vdw_refined	0.112
r_chiral_restr	0.091
r_metal_ion_refined	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	193

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing