4PMJ | pdb_00004pmj

Crystal structure of a putative oxidoreductase from Sinorhizobium meliloti 1021 in complex with NADP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.2 ul of 14 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-II condition #42 (1.1 M Ammonium Tartrate Dibasic pH 7.0) 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 solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.324	α = 90
b = 78.897	β = 90
c = 79.563	γ = 90

Symmetry
Space Group	P 21 21 21

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		2014-03-20	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)	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	97.9	0.136	0.136	11.4	6	14760	14450		-3	25.7

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	2.2	2.24	85.7		0.457	1.9	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	50	13677	731	97.87	0.16977	0.16725	0.18	0.21676	0.23	RANDOM	30.852

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]
0.02			1		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_3_deg	14.328
r_dihedral_angle_4_deg	12.063
r_dihedral_angle_1_deg	5.768
r_long_range_B_refined	5.72
r_long_range_B_other	5.719
r_scangle_other	2.005
r_angle_refined_deg	1.662
r_scbond_it	1.304
r_scbond_other	1.301
r_mcangle_other	1.258
r_mcangle_it	1.257
r_angle_other_deg	0.947
r_mcbond_it	0.749
r_mcbond_other	0.745
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
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	2127
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	54

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
HKL-3000	data scaling
SHELXDE	phasing
MLPHARE	phasing
DM	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction