3BVD | pdb_00003bvd

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	297	6-9% PEG 2000, 50mM KCl, 7.5-30mM bis-Tris pH 7.0, 6.5mM nonyl-B-D-glucopyranoside , VAPOR DIFFUSION, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.65

Symmetry
Space Group	P 41 21 2

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 315	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2007-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979	SSRL	BL9-1

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	3.37	27.16	99.7	0.068	8.1	4.5	16390	16341			108.222

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)
	3.37	3.55	100		0.463	1.8	4.8	2339

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-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 1XME	3.37	26.96	16297	16329	823	99.84	0.2922	0.27	0.3355	0.32	RANDOM	85.48

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]
-0.04			-0.04		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.125
r_dihedral_angle_3_deg	19.271
r_dihedral_angle_4_deg	18.676
r_dihedral_angle_1_deg	5.323
r_angle_refined_deg	1.304
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.277
r_metal_ion_refined	0.211
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.125
r_dihedral_angle_3_deg	19.271
r_dihedral_angle_4_deg	18.676
r_dihedral_angle_1_deg	5.323
r_angle_refined_deg	1.304
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.277
r_metal_ion_refined	0.211
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.127
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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	5907
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	118