Experiment: 2OQJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OP3	pdb entry 1op3 with carbohydrate removed from the Fab binding site

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	1.33M Na/K phosphate, 0.2M isopropanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.264	α = 90
b = 171.348	β = 105.64
c = 119.568	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	CCD	ADSC QUANTUM 4		2003-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	48.7	98.2	0.115	9.8	3.1	62018	62018		-3	58.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	97.9		0.476	2.5	3.1	3095

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1op3 with carbohydrate removed from the Fab binding site	2.8	48.7	58837	58837	3138	98.16	0.236	0.236	0.23396	0.27461	RANDOM	69.115

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]
9.14		7.85	-5.87		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.125
r_dihedral_angle_4_deg	18.271
r_dihedral_angle_3_deg	15.499
r_dihedral_angle_1_deg	5.266
r_angle_refined_deg	1.014
r_scangle_it	0.677
r_scbond_it	0.409
r_nbtor_refined	0.295
r_mcangle_it	0.272
r_nbd_refined	0.179

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.125
r_dihedral_angle_4_deg	18.271
r_dihedral_angle_3_deg	15.499
r_dihedral_angle_1_deg	5.266
r_angle_refined_deg	1.014
r_scangle_it	0.677
r_scbond_it	0.409
r_nbtor_refined	0.295
r_mcangle_it	0.272
r_nbd_refined	0.179
r_symmetry_hbond_refined	0.174
r_symmetry_vdw_refined	0.17
r_mcbond_it	0.156
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13685
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.