3K7T | pdb_00003k7t

Crystal structure of apo-form 6-hydroxy-L-nicotine oxidase, crystal form P3121

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K7M	PDB ENTRY 3K7M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.1M Hepes, 1.5M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.7	73.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.957	α = 90
b = 122.957	β = 90
c = 199.918	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2002-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.85	20	99.2	0.078	0.078	25.3	7.5	41415	41084		2	72.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.85	2.9	100		0.75	0.75	2	7.5	2038

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLREP	THROUGHOUT	PDB ENTRY 3K7M	2.85	16.6	39197	38462	2035	98.14	0.27776	0.27549	0.32	0.32118	0.32	RANDOM	72.942

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]
3.72	1.86		3.72		-5.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.675
r_dihedral_angle_3_deg	18.815
r_dihedral_angle_4_deg	17.515
r_dihedral_angle_1_deg	7.599
r_scangle_it	4.256
r_scbond_it	2.467
r_mcangle_it	1.853
r_angle_refined_deg	1.781
r_mcbond_it	1.021
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.294
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.161
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6540
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	192

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling