5T57 | pdb_00005t57

Crystal Structure of a Semialdehyde dehydrogenase NAD-binding Protein from Cupriavidus necator in Complex with Calcium and NAD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C24

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M CaCl2, 20 (w/v) PEB-3350, 5 mM Mg, 5 mM NAD+

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.903	α = 90
b = 71.14	β = 90
c = 47.649	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 315	Diamond	2016-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	1.646	19.956	99.9	0.114	8.7	6.9		36952

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.73	100		0.919	0.8	6.9

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 (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	3C24	1.65	19.956	35109	1792	99.82	0.1742	0.1727	0.18	0.2031	0.21	RANDOM	24.885

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]
-1.13			0.47		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_4_deg	15.084
r_dihedral_angle_3_deg	13.666
r_dihedral_angle_1_deg	5.712
r_mcangle_it	3.15
r_mcbond_it	2.249
r_mcbond_other	2.241
r_angle_refined_deg	1.956
r_angle_other_deg	1.096
r_chiral_restr	0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_4_deg	15.084
r_dihedral_angle_3_deg	13.666
r_dihedral_angle_1_deg	5.712
r_mcangle_it	3.15
r_mcbond_it	2.249
r_mcbond_other	2.241
r_angle_refined_deg	1.956
r_angle_other_deg	1.096
r_chiral_restr	0.131
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2123
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	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.