2RH8 | pdb_00002rh8

Structure of apo anthocyanidin reductase from vitis vinifera

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C29	PDB ENTRY 2C29

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	NH4 acetate 150 mM, PEG 3350, Hepes 100 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.47	α = 90
b = 50.47	β = 90
c = 440.406	γ = 120

Symmetry
Space Group	P 61 2 2

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	ADSC QUANTUM 210	MIRRORS	2007-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.22	43.727	96.4	0.087	0.087	5.6	11.7		17253			42.07

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)
	2.22	2.34	98.8		0.343	0.343	2	12.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2C29	2.22	30	17114	17114	851	95.7	0.203	0.199	0.21	0.27	0.29	RANDOM	34.07

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]
0.88	0.44		0.88		-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.824
r_dihedral_angle_4_deg	19.97
r_dihedral_angle_3_deg	14.543
r_scangle_it	5.915
r_dihedral_angle_1_deg	5.765
r_mcangle_it	4.565
r_scbond_it	4.303
r_mcbond_it	3.21
r_angle_refined_deg	2.068
r_angle_other_deg	1.229
r_mcbond_other	0.695
r_symmetry_hbond_refined	0.345
r_nbd_refined	0.21
r_nbd_other	0.184
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_other	0.175
r_chiral_restr	0.118
r_symmetry_vdw_refined	0.118
r_nbtor_other	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2309
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction