2IOD | pdb_00002iod

Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site

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	VAPOR DIFFUSION, HANGING DROP	6.9	298	50mM NaCl, 29% PEG3350, 100mM Hepes, 3mM NaN3, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.231	α = 90
b = 177.958	β = 104.77
c = 92.597	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	100	CCD	ADSC QUANTUM 210	MIRRORS	2005-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0400	ESRF	ID29

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	2.06	89.535	99	0.093	0.093	4	3.2		89953			30

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)
	2.06	2.17	94.1		0.505	0.505	2.1	2.5	12398

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 (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	2.06	89.44	89894	4501	98.88	0.193	0.193	0.189	0.2	0.257	0.26	RANDOM	35.307

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]
0.17		-0.85	2.1		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.877
r_dihedral_angle_3_deg	15.464
r_dihedral_angle_4_deg	15.034
r_dihedral_angle_1_deg	5.81
r_angle_other_deg	4.316
r_mcangle_it	3.877
r_scangle_it	3.828
r_scbond_it	2.778
r_mcbond_it	2.568
r_angle_refined_deg	1.925
r_symmetry_hbond_refined	0.263
r_nbd_other	0.235
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.187
r_symmetry_vdw_other	0.175
r_nbtor_other	0.113
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_xyhbond_nbd_other	0.008
r_gen_planes_other	0.007
r_gen_planes_refined	0.005
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9981
Nucleic Acid Atoms
Solvent Atoms	768
Heterogen Atoms	376

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
MOSFLM	data reduction