5BSH | pdb_00005bsh

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

X-RAY DIFFRACTION

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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
2.94	58.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.489	α = 67.65
b = 100.928	β = 85.46
c = 101.925	γ = 89.44

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		2014-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9786	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	40	97.7	0.069	0.086	0.05	9	2.6		183949

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	2.1	2.14	96.7		0.482	0.608	0.365	0.775	1.9	2.6	9112

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	FREE R-VALUE	2IZZ, 5BSE	2.1	40	182006	1941	97	0.18	0.18	0.1854	0.197	0.2004	RANDOM	74

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]
-1.61	-0.4	-1.78	1.6	1.54	0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.908
r_dihedral_angle_4_deg	15.423
r_dihedral_angle_3_deg	13.86
r_dihedral_angle_1_deg	5.782
r_mcangle_it	5.647
r_mcbond_it	4.111
r_mcbond_other	4.104
r_angle_refined_deg	1.6
r_angle_other_deg	1.365
r_chiral_restr	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_bond_other_d	0.01
r_gen_planes_other	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19678
Nucleic Acid Atoms
Solvent Atoms	695
Heterogen Atoms	80

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction