5BSF

Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR) in complex with NAD+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IZZ	2IZZ, 5BSE
experimental model	PDB	5BSE	2IZZ, 5BSE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	Morpheus screen (Molecular Dimensions) A7 solution (100 mM HEPES/MOPS buffer pH 7.5, 10% polyethylene glycol 4000, 20% glycerol, 30 mM MgCl2 and 30 mM CaCl2).

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.54	α = 67.5
b = 100.78	β = 85.86
c = 101.61	γ = 89.78

Symmetry
Space Group	P 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	ADSC QUANTUM 315r		2014-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9790	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	40	97.4	0.045	0.053	17.69	3.7		266309		-3	35.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	96.2		0.64	0.75	1.96	3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2IZZ, 5BSE	1.85	39.13	264178	2131	97.51	0.156	0.155	0.177	RANDOM	41.4

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]
-1.1	-0.42	-1.23	-0.47	0.91	1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.699
r_dihedral_angle_4_deg	16.244
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_1_deg	5.998
r_mcangle_it	4.119
r_mcbond_it	2.95
r_mcbond_other	2.949
r_angle_other_deg	1.972
r_angle_refined_deg	1.864
r_chiral_restr	0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.699
r_dihedral_angle_4_deg	16.244
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_1_deg	5.998
r_mcangle_it	4.119
r_mcbond_it	2.95
r_mcbond_other	2.949
r_angle_other_deg	1.972
r_angle_refined_deg	1.864
r_chiral_restr	0.112
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.01
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19785
Nucleic Acid Atoms
Solvent Atoms	1670
Heterogen Atoms	580

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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 R01GM133198.