4L9D

Crystal structure of the PKD1 domain from Vibrio cholerae metalloprotease PrtV

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	1.2 M sodium citrate and 20% (w/v) PEG 8K, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.8	α = 90
b = 50.833	β = 90
c = 67.297	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	ADSC QUANTUM 315r		2011-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0398	ESRF	ID23-1

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	1.1	12	99	0.06	16.7			58243	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	1.1	1.15	96.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.1	12	55335	2958	98.95	0.11099	0.10947	0.1404	RANDOM	10.249

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]
-0.12			0.14		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.461
r_sphericity_free	36.289
r_dihedral_angle_1_deg	13.44
r_dihedral_angle_3_deg	11.926
r_sphericity_bonded	11.819
r_dihedral_angle_4_deg	10.466
r_rigid_bond_restr	6.142
r_long_range_B_refined	4.789
r_long_range_B_other	4.095
r_scangle_other	4.085
r_scbond_other	3.327
r_scbond_it	3.326
r_mcbond_it	2.737
r_mcbond_other	2.468
r_angle_refined_deg	2.192
r_mcangle_other	2.11
r_mcangle_it	2.024
r_angle_other_deg	1.012
r_chiral_restr	0.129
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.004
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1233
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	14

Software

Software
Software Name	Purpose
XDS	data scaling
Auto-Rickshaw	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling