5AK7

Structure of wt Porphyromonas gingivalis peptidylarginine deiminase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				22% PEG3350, 0.1M BIS-TRIS PH 5.5, 0.1M LITHIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.86	α = 90
b = 84.66	β = 92.5
c = 55.66	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	1.46	65.08	97.9	0.04	14.3	3.4		79913		1

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	1.46	1.5	95		0.49	2.2	3.2

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	1.46	65.08	75992	3920	97.77	0.12952	0.12822	0.15402	RANDOM	19.083

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]
-0.59		0.04	1.08		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.511
r_sphericity_free	26.354
r_dihedral_angle_4_deg	11.531
r_dihedral_angle_3_deg	10.451
r_sphericity_bonded	8.634
r_dihedral_angle_1_deg	5.951
r_scbond_it	2.138
r_mcangle_it	1.41
r_angle_refined_deg	1.27
r_mcbond_it	1.047
r_mcbond_other	1.047
r_rigid_bond_restr	0.958
r_angle_other_deg	0.89
r_chiral_restr	0.078
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3289
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	85

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Rosetta	phasing