5MSP | pdb_00005msp

Structure of the unmodified PCP-R didomain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADP, F2221 form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MSO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	CARsr PCP-Red crystals were obtained in 0.1 M sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003.

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.37	α = 90
b = 137.68	β = 90
c = 202.08	γ = 90

Symmetry
Space Group	F 2 2 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	PIXEL	DECTRIS PILATUS 6M-F		2016-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.41	101.04	99	0.11	1	8	5.4		36214

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.41	2.5	99.5		0.6

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	5MSO	2.41	101.04	34488	1728	99.24	0.18117	0.17894	0.19	0.22697	0.23	RANDOM	66.76

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]
6.26			-1.95		-4.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.685
r_dihedral_angle_4_deg	20.761
r_dihedral_angle_3_deg	17.774
r_long_range_B_refined	12.018
r_long_range_B_other	12.016
r_scangle_other	10.015
r_mcangle_it	7.48
r_mcangle_other	7.479
r_scbond_other	6.591
r_scbond_it	6.59
r_dihedral_angle_1_deg	6.555
r_mcbond_it	5.346
r_mcbond_other	5.346
r_angle_refined_deg	1.912
r_angle_other_deg	1.116
r_chiral_restr	0.118
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	3911
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing