8XS1 | pdb_00008xs1

Crystal structure of Fab fragment of anti-osteocalcin antibody KTM219 complexed with C-terminal peptide antigen

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5X5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.4	297	0.07 M Citric acid, 0.03 M BIS-TRIS propane, 16% Polyethylene glycol 3,350, by using random Microseed Matrix Screening (rMMS) method

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.88	α = 90
b = 67.489	β = 90
c = 138.655	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	95	CCD	ADSC QUANTUM 270		2015-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.3	50	99.1	0.151	0.165	0.066	5.3	6.1		18912

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	2.3	2.38	99.6		0.769	0.835	0.32	0.836	2.6	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5X5X	2.3	50	17875	984	98.85	0.20143	0.19897	0.2059	0.24781	0.2533	RANDOM	39.498

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]
-3.37			1.69		1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.267
r_dihedral_angle_3_deg	16.193
r_dihedral_angle_4_deg	15.208
r_dihedral_angle_1_deg	7.489
r_long_range_B_refined	7.403
r_long_range_B_other	7.401
r_scangle_other	4.656
r_mcangle_it	3.895
r_mcangle_other	3.894
r_scbond_it	2.873
r_scbond_other	2.872
r_mcbond_other	2.487
r_mcbond_it	2.486
r_angle_refined_deg	1.654
r_angle_other_deg	0.979
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.006
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	3319
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

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