3V4C | pdb_00003v4c

Crystal structure of a semialdehyde dehydrogenase from Sinorhizobium meliloti 1021

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EYY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2M Sodium acetate trihydrate, 0.1M Tris hydrochloride, 30% PEG 4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.197	α = 90
b = 46.079	β = 104.76
c = 117.404	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M	mirrors	2011-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.91	50	99.6	0.038	13.5	6.3	75865	75865

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	1.91	1.98	98.3		0.11	9	5.1	7416

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1EYY	1.91	46.29	75865	71947	3801	99.39	0.17406	0.1714	0.17	0.22522	0.23	RANDOM	27.699

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.901
r_dihedral_angle_4_deg	20.449
r_dihedral_angle_3_deg	15.11
r_dihedral_angle_1_deg	6.401
r_scangle_it	5.866
r_scbond_it	3.799
r_mcangle_it	2.055
r_angle_refined_deg	2.001
r_mcbond_it	1.231
r_chiral_restr	0.151

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.901
r_dihedral_angle_4_deg	20.449
r_dihedral_angle_3_deg	15.11
r_dihedral_angle_1_deg	6.401
r_scangle_it	5.866
r_scbond_it	3.799
r_mcangle_it	2.055
r_angle_refined_deg	2.001
r_mcbond_it	1.231
r_chiral_restr	0.151
r_bond_refined_d	0.025
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7406
Nucleic Acid Atoms
Solvent Atoms	677
Heterogen Atoms	15

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
ARP/wARP	model building
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	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.