2OME

Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MX3	PDB entries 1MX3, 1HL3
experimental model	PDB	1HL3	PDB entries 1MX3, 1HL3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.2M KSCN, 0.1M BIS-TRIS PROPANE, 20% PEG3350, 10% ETHYLENE GLYCOL, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.754	α = 90
b = 141.574	β = 98.93
c = 138.215	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	MARMOSAIC 225 mm CCD		2006-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99991	SLS	X10SA

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	2.77	43.31	100	0.148	0.162	11.6	6.1		84796		2

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)
1	2.77	2.92	100		0.81	0.89	2	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 entries 1MX3, 1HL3	2.8	43.31	2	84796	78004	4104	99.98	0.2098	0.20733	0.21	0.25736	0.26	RANDOM	40.724

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]
1.63		-0.55	-4.83		3.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.744
r_dihedral_angle_3_deg	17.854
r_dihedral_angle_4_deg	17.542
r_dihedral_angle_1_deg	6.348
r_scangle_it	2.014
r_angle_refined_deg	1.458
r_scbond_it	1.253
r_angle_other_deg	1.116
r_mcangle_it	0.548
r_mcbond_it	0.349
r_symmetry_hbond_refined	0.27
r_nbd_refined	0.211
r_nbd_other	0.195
r_nbtor_refined	0.184
r_symmetry_vdw_refined	0.181
r_symmetry_vdw_other	0.178
r_xyhbond_nbd_refined	0.149
r_mcbond_other	0.128
r_nbtor_other	0.087
r_chiral_restr	0.075
r_xyhbond_nbd_other	0.023
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	20223
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	352

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing