2NNL | pdb_00002nnl

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	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
2.45	49.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.825	α = 90
b = 90.143	β = 90
c = 93.297	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	mirrors	2005-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.04	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	2.1	64.827	85.9	0.136	0.136	3.7	5.4	37210	37210			34.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.21	89.1		1.9	5.3	5566

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 (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	2c29	2.1	64.82	37159	37159	1899	84.65	0.192	0.192	0.19	0.18	0.242	0.24	RANDOM	37.017

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]
-0.33			2.47		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.562
r_dihedral_angle_4_deg	16.11
r_dihedral_angle_3_deg	14.509
r_dihedral_angle_1_deg	5.187
r_scangle_it	2.537
r_mcangle_it	2.534
r_scbond_it	1.683
r_mcbond_it	1.519
r_angle_refined_deg	1.271
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.562
r_dihedral_angle_4_deg	16.11
r_dihedral_angle_3_deg	14.509
r_dihedral_angle_1_deg	5.187
r_scangle_it	2.537
r_mcangle_it	2.534
r_scbond_it	1.683
r_mcbond_it	1.519
r_angle_refined_deg	1.271
r_nbtor_refined	0.304
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5027
Nucleic Acid Atoms
Solvent Atoms	558
Heterogen Atoms	138

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
AMoRE	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.