5BSF

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

X-RAY DIFFRACTION

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.