4ZQB | pdb_00004zqb

Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PP8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 ul of 10.5 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition # 23 (0.1M Bis-Tris, 25%w/v PEG 3350, 0.2M Li sulfate pH=6.5 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin and 10 mM NADP solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.489	α = 90
b = 71.489	β = 90
c = 244.364	γ = 120

Symmetry
Space Group	P 61

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	Beryllium Lenses	2014-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	50	99.3	0.161	0.161	0.171	0.073	4.7	6.2	60347	59896		-3	23.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	97.1		0.428	0.649	2	6.2	2955

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	3PP8	1.85	50	59625	2948	99.41	0.1665	0.1649	0.17	0.1997	0.21	RANDOM	27.931

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]
-0.35	-0.18		-0.35		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.836
r_dihedral_angle_4_deg	19.48
r_dihedral_angle_3_deg	12.205
r_dihedral_angle_1_deg	5.439
r_angle_refined_deg	1.565
r_angle_other_deg	1.263
r_mcangle_it	0.938
r_mcbond_other	0.585
r_mcbond_it	0.584
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4762
Nucleic Acid Atoms
Solvent Atoms	694
Heterogen Atoms	139

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
Coot	model building
REFMAC	refinement
HKL-3000	phasing
MOLREP	phasing
HKL-3000	data scaling
HKL-3000	data reduction
BLU-MAX	data collection