2H5G | pdb_00002h5g

Crystal structure of human pyrroline-5-carboxylate synthetase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	1% PEG 3350, 1.0M (NH4)2SO4, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.022	α = 90
b = 137.402	β = 90
c = 72.057	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARRESEARCH		2005-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97925	SLS	X10SA

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	2.25	91.29	98.2	0.056	0.033		6.89	58292	57217

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.35	88.3		0.261	0.205	4.39	3.67	11978

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.25	46.56	57217	54237	2890	98.1	0.23248	0.23248	0.23037	0.262	0.27211	0.2987	RANDOM	59.168

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]
-2.79			-0.14		2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.466
r_dihedral_angle_4_deg	19.305
r_dihedral_angle_3_deg	15.463
r_scangle_it	8.077
r_scbond_it	6.302
r_dihedral_angle_1_deg	5.52
r_mcangle_it	3.549
r_mcbond_it	2.409
r_angle_refined_deg	1.478
r_nbtor_refined	0.297
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.208
r_symmetry_hbond_refined	0.121
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.105
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6348
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
SOLVE	phasing