Experiment: 3C0J

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	285	1.8M K2HPO4 (pH 10.0), 6% w/v N-octyl-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.04

Symmetry
Space Group	P 31 2 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU RAXIS IV++		2006-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	34.79	98.5	0.114	7.8	3.96	36400	36400

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	98.9		0.393	2.8

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	PDB ENTRY 1YXC	2.4	31.49	34563	1818	100	0.1734	0.1702	0.18	0.23729	0.24	RANDOM	32.2

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]
-0.35	-0.17		-0.35		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.619
r_dihedral_angle_4_deg	18.22
r_dihedral_angle_3_deg	16.412
r_dihedral_angle_1_deg	7.041
r_scangle_it	4.12
r_scbond_it	2.674
r_angle_refined_deg	1.765
r_mcangle_it	1.471
r_angle_other_deg	1.095
r_mcbond_it	0.789

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.619
r_dihedral_angle_4_deg	18.22
r_dihedral_angle_3_deg	16.412
r_dihedral_angle_1_deg	7.041
r_scangle_it	4.12
r_scbond_it	2.674
r_angle_refined_deg	1.765
r_mcangle_it	1.471
r_angle_other_deg	1.095
r_mcbond_it	0.789
r_symmetry_vdw_other	0.293
r_symmetry_hbond_refined	0.231
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.222
r_nbd_other	0.205
r_mcbond_other	0.182
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.165
r_metal_ion_refined	0.148
r_chiral_restr	0.099
r_nbtor_other	0.093
r_bond_refined_d	0.021
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4360
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	30

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3C0J | pdb_00003c0j