1Y56

Crystal structure of L-proline dehydrogenase from P.horikoshii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	10.5	298	CAPS, NaH2PO4, K2HPO4, Li2SO4, pH 10.5, EVAPORATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 172.219	α = 90
b = 172.219	β = 90
c = 175.398	γ = 120

Symmetry
Space Group	P 64 2 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	ADSC QUANTUM 210		2003-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	48.41	98.7			38014	37913	1	1

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	2.8	2.96	93.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MIR	THROUGHOUT	2.86	19.85	1	38014	31021	1655	100	0.18396	0.1817	0.22557	RANDOM	35.551

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]
2.08	1.04		2.08		-3.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.481
r_dihedral_angle_3_deg	21.509
r_angle_other_deg	21.127
r_dihedral_angle_4_deg	18.802
r_dihedral_angle_1_deg	9.137
r_scangle_it	2.362
r_angle_refined_deg	1.564
r_scbond_it	1.396
r_mcangle_it	0.921
r_mcbond_it	0.711
r_nbd_other	0.502
r_nbtor_refined	0.322
r_nbtor_other	0.318
r_bond_other_d	0.27
r_symmetry_hbond_refined	0.256
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.12
r_mcbond_other	0.115
r_gen_planes_other	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6805
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	136

Software

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