2Z5Z | pdb_00002z5z

Crystal structure of the complex of buffalo Lactoperoxidase with fluoride ion at 3.5A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O86	PDB entry 2O86

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	290	TRIS-HCL, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.127	α = 90
b = 80.739	β = 102.94
c = 77.699	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	MARRESEARCH	Mirror	2007-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

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	3.5	75.81	83.6	0.129	3.9	3.1		6641			64.2

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	3.5	3.62	87.7		0.184	1.9	3.1	6641

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 2O86	3.5	75.81	6641	324	83.19	0.22182	0.22117	0.21	0.23484	0.22	RANDOM	27.023

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]
-0.71		-0.93	-4.6		4.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.636
r_dihedral_angle_3_deg	18.978
r_dihedral_angle_4_deg	15.72
r_dihedral_angle_1_deg	2.376
r_angle_refined_deg	1.991
r_symmetry_hbond_refined	0.331
r_nbtor_refined	0.327
r_symmetry_vdw_refined	0.286
r_nbd_refined	0.247
r_xyhbond_nbd_refined	0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.636
r_dihedral_angle_3_deg	18.978
r_dihedral_angle_4_deg	15.72
r_dihedral_angle_1_deg	2.376
r_angle_refined_deg	1.991
r_symmetry_hbond_refined	0.331
r_nbtor_refined	0.327
r_symmetry_vdw_refined	0.286
r_nbd_refined	0.247
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.131
r_metal_ion_refined	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_mcbond_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	194

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	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.