4MSF | pdb_00004msf

Crystal structure of the complex of goat lactoperoxidase with 3-hydroxymethyl phenol at 1.98 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	Sodium nitrate, PEG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.766	α = 90
b = 80.356	β = 102.71
c = 75.76	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	77	CCD	MARRESEARCH	mirror	2013-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.98	80.36	95.8	0.0743	3.5		41800	41862

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	1.98	2.05	98.9		0.1646	3.5

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	3GC1	1.98	54.39	40586	2148	97.39	0.19402	0.19166	0.2	0.23754	0.24	RANDOM	39.715

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]
-0.02		-1.19	-0.08		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.974
r_dihedral_angle_3_deg	16.037
r_dihedral_angle_4_deg	13.828
r_long_range_B_refined	7.183
r_long_range_B_other	7.183
r_dihedral_angle_1_deg	6.989
r_scangle_other	2.007
r_mcangle_it	1.935
r_mcangle_other	1.935
r_angle_refined_deg	1.77
r_scbond_it	1.304
r_scbond_other	1.304
r_mcbond_it	1.129
r_mcbond_other	1.125
r_angle_other_deg	0.888
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4757
Nucleic Acid Atoms
Solvent Atoms	504
Heterogen Atoms	153

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling