4R5M

Crystal structure of Vc-Aspartate beta-semialdehyde-dehydrogenase with NADP and 4-Nitro-2-Phosphono-Benzoic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q0E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	15-20% PEG 3350, 0.1 M Na-citrate (pH 6.5), 0.1 M Na-acetate, 10 mM DTT, 3% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.353	α = 90
b = 107.353	β = 90
c = 152.837	γ = 90

Symmetry
Space Group	P 43 21 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	MARMOSAIC 300 mm CCD	double crystal monochromator and K-B pair of biomorph mirrors	2014-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.88	50	97.7	0.123	10.6	4.9	73060	71382	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.95	86.6		0.386	3.5	4.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3Q0E	1.89	87.85	73062	67739	3610	98.84	0.17058	0.16916	0.19696	RANDOM	31.393

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]
-0.57			-0.57		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.9
r_dihedral_angle_4_deg	18.375
r_dihedral_angle_3_deg	11.273
r_dihedral_angle_1_deg	5.68
r_long_range_B_refined	5.291
r_long_range_B_other	4.916
r_scangle_other	2.748
r_mcangle_it	1.983
r_mcangle_other	1.983
r_scbond_other	1.694
r_scbond_it	1.688
r_mcbond_it	1.267
r_mcbond_other	1.264
r_angle_refined_deg	1.25
r_angle_other_deg	0.757
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5654
Nucleic Acid Atoms
Solvent Atoms	601
Heterogen Atoms	129

Software

Software
Software Name	Purpose
REFMAC	refinement