9NJY | pdb_00009njy

Terminal two domains of ClfA002 with bound Fab of AZD7745

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N67

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	295	9 mM MgCl2, 90 mM HEPES, 18% PEG 6000 (w/v), 1% Glycerol (v/v)

Crystal Properties
Matthews coefficient	Solvent content
2.7	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.582	α = 90
b = 66.164	β = 90.583
c = 107.875	γ = 90

Symmetry
Space Group	P 1 21 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		2015-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.58	35	99.9	0.06	0.999	16.3	6.6		117495

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.58			0.886

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	THROUGHOUT	1.58	25.001	116697	5792	99.839	0.2	0.1986	0.2093	0.219	0.2254	20.624

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]
-0.098		-1.329	0.84		-0.715

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.931
r_dihedral_angle_3_deg	10.139
r_dihedral_angle_1_deg	6.759
r_dihedral_angle_2_deg	4.51
r_lrange_it	3.571
r_lrange_other	3.475
r_scangle_it	2.249
r_scangle_other	2.249
r_mcangle_it	1.724
r_mcangle_other	1.724
r_scbond_other	1.373
r_scbond_it	1.372
r_angle_refined_deg	1.056
r_mcbond_it	1.023
r_mcbond_other	1.023
r_angle_other_deg	0.385
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.19
r_nbd_refined	0.188
r_nbtor_refined	0.169
r_nbd_other	0.147
r_symmetry_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.082
r_symmetry_nbd_refined	0.071
r_chiral_restr	0.053
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5641
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	12

Software

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