5X5X

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.6 M sodium formate, 29% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.8	α = 90
b = 71.472	β = 90
c = 96.882	γ = 90

Symmetry
Space Group	P 21 2 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 315r		2014-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	50	98.8	0.066	0.071	0.027	12.5	6.8		35733			25.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	97.5		0.484	0.522	0.194	0.918	4.23	6.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4KUZ	1.9	50	33891	1786	98.62	0.1828	0.1806	0.2235	RANDOM	31.038

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]
-0.95			0.3		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.011
r_dihedral_angle_4_deg	17.487
r_dihedral_angle_3_deg	13.377
r_dihedral_angle_1_deg	6.779
r_angle_refined_deg	1.539
r_angle_other_deg	0.914
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.011
r_dihedral_angle_4_deg	17.487
r_dihedral_angle_3_deg	13.377
r_dihedral_angle_1_deg	6.779
r_angle_refined_deg	1.539
r_angle_other_deg	0.914
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3271
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	83

Software

Software
Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.