5FCF

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		294	40mM KH2PO4, 20% Glycerol, 14% PEG 8000, 2mM MnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.962	α = 90
b = 104.284	β = 90
c = 112.324	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD	x-ray mirror	2015-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE BL-21	0.97947	RRCAT INDUS-2	BL-21

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	1.85	47.29	99.8	0.102	14	6.8		82603

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	99.4		0.871	2.4	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.85	45	78448	4080	99.73	0.16088	0.15907	0.19591	RANDOM	24.237

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]
-0.03			-0.34		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.829
r_dihedral_angle_4_deg	20.813
r_dihedral_angle_3_deg	12.548
r_dihedral_angle_1_deg	6.697
r_long_range_B_refined	4.971
r_long_range_B_other	4.889
r_scangle_other	3.459
r_angle_refined_deg	2.369
r_scbond_it	2.285
r_scbond_other	2.284
r_mcangle_other	1.9
r_mcangle_it	1.899
r_mcbond_it	1.383
r_mcbond_other	1.383
r_angle_other_deg	1.161
r_chiral_restr	0.155
r_bond_refined_d	0.027
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5988
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
PHENIX	model building
PHASER	phasing
Aimless	data scaling
XDS	data processing
MAR345dtb	data collection