5C5I | pdb_00005c5i

Crystal structure of NADP-dependent dehydrogenase from Rhodobacter sphaeroides

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZQB

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 # 72 (20%w/v PEG 3350, 0.2M Li nitrate) 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

Crystal Properties
Matthews coefficient	Solvent content
2	38.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.048	α = 90
b = 80.085	β = 93.69
c = 61.33	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	CCD	MARMOSAIC 300 mm CCD		2014-11-06	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	2.2	50	96.4	0.074	0.074	0.085	0.04	8.7	4.4		26059		-3	41.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	79.5		0.527	0.602	0.286	0.893	2.2	3.9	1079

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	4ZQB	2.2	50	26059	1253	96.36	0.1973	0.1945	0.2	0.252	0.25	RANDOM	62.532

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]
-1.11		1.16	7.09		-6.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.004
r_dihedral_angle_4_deg	22.018
r_dihedral_angle_3_deg	13.702
r_dihedral_angle_1_deg	5.807
r_mcangle_it	2.457
r_angle_refined_deg	1.657
r_mcbond_other	1.58
r_mcbond_it	1.579
r_angle_other_deg	1.271
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4537
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

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