1YQG | pdb_00001yqg

Crystal structure of a pyrroline-5-carboxylate reductase from neisseria meningitides mc58

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	AMMONIUM SULFATE, HEPES, PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.526	α = 90
b = 49.845	β = 90
c = 65.534	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	CUSTOM-MADE		2004-07-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97984, 0.97970	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.61	50	69	0.102	24.66	9.5	38574	26616

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.67	0.7

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	MAD	THROUGHOUT	1.9	50	22585	22303	1205	98.75	0.19727	0.19727	0.19495	0.1931	0.24059	0.2377	RANDOM	32.446

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]
1.03			-0.36		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.068
r_dihedral_angle_4_deg	20.031
r_dihedral_angle_3_deg	16.056
r_dihedral_angle_1_deg	5.567
r_scangle_it	5.276
r_scbond_it	3.881
r_mcangle_it	1.584
r_angle_refined_deg	1.516
r_mcbond_it	1.092
r_symmetry_hbond_refined	0.337
r_nbtor_refined	0.298
r_nbd_refined	0.241
r_symmetry_vdw_refined	0.238
r_xyhbond_nbd_refined	0.206
r_chiral_restr	0.109
r_bond_refined_d	0.018
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	1980
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
HKL-3000	phasing