Experiment: 2P3X

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BT1	Polyphenol oxidase of sweet potato (1BT1)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.03	α = 90
b = 120.77	β = 90
c = 140.8	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	298	CCD	ADSC QUANTUM 210	Monochromator	2006-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.1	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50			6.96		26382

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	97.8		0.487	2.9	5.41	26382

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Polyphenol oxidase of sweet potato (1BT1)	2.2	37.06	23748	2598	99.75	0.2057	0.20572	0.20053	0.25205	RANDOM	39.449

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]
0.01					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.535
r_dihedral_angle_3_deg	20.474
r_dihedral_angle_4_deg	18.507
r_dihedral_angle_1_deg	18.187
r_scangle_it	4.867
r_scbond_it	3.27
r_angle_refined_deg	2.545
r_mcangle_it	2.153
r_mcbond_it	1.313
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.535
r_dihedral_angle_3_deg	20.474
r_dihedral_angle_4_deg	18.507
r_dihedral_angle_1_deg	18.187
r_scangle_it	4.867
r_scbond_it	3.27
r_angle_refined_deg	2.545
r_mcangle_it	2.153
r_mcbond_it	1.313
r_nbtor_refined	0.317
r_chiral_restr	0.277
r_nbd_refined	0.247
r_symmetry_vdw_refined	0.23
r_symmetry_hbond_refined	0.2
r_xyhbond_nbd_refined	0.161
r_bond_refined_d	0.024
r_metal_ion_refined	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2713
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	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.