9B98 | pdb_00009b98

Crystal structure of the human PAD2 protein bound to small molecule

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Internal apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293.15	0.1M Magnesium acetate, 50mM MES pH5.5, 9-16% 2-methyl 2, 4-pentane diol

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 201.71	α = 90
b = 52.78	β = 105.709
c = 76.59	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 EIGER2 X 9M		2018-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.003	97.088	92.2	0.038	0.045	0.025	0.999	16.3	3.3		26935

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.003	2.276	75.5		0.759	0.903	0.483	0.617	1.7	3.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.003	97.088	26935	1358	51.213	0.189	0.1857	0.195	0.2575	0.2629	59.135

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]
-0.08		-0.205	0.259		-0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.487
r_dihedral_angle_2_deg	18.017
r_dihedral_angle_6_deg	16.064
r_lrange_it	12.552
r_lrange_other	12.551
r_dihedral_angle_1_deg	9.209
r_scangle_it	8.262
r_scangle_other	8.26
r_mcangle_it	8.1
r_mcangle_other	8.099
r_mcbond_it	5.48
r_mcbond_other	5.471
r_scbond_it	5.426
r_scbond_other	5.425
r_angle_refined_deg	1.51
r_angle_other_deg	0.516
r_xyhbond_nbd_refined	0.23
r_nbd_refined	0.224
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.174
r_nbd_other	0.171
r_symmetry_nbd_refined	0.167
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4805
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing