2VUV | pdb_00002vuv

Crystal structure of Codakine at 1.3A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		HOMOLOGY MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2 M DI-AMMONIUM CITRATE PH 5, 20% W/V PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.908	α = 90
b = 30.395	β = 133.86
c = 67.088	γ = 90

Symmetry
Space Group	C 1 2 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 CCD	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

Data Collection

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	1.3	33.11	89.7	0.03	12.1	3.3		26746		2	10.39

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	1.3	1.37	52.5		0.32	2.1	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	HOMOLOGY MODEL	1.3	27.63	2	26746	1370	89.2	0.145	0.144	0.15	0.161	0.17	RANDOM	8.84

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]
0.943		0.552	-0.306		0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.215
r_dihedral_angle_4_deg	16.083
r_dihedral_angle_3_deg	11.517
r_dihedral_angle_1_deg	6.361
r_scangle_it	3.518
r_scbond_it	2.421
r_angle_refined_deg	1.724
r_mcangle_it	1.664
r_mcbond_it	1.187
r_angle_other_deg	0.955
r_symmetry_vdw_refined	0.554
r_symmetry_vdw_other	0.36
r_nbd_refined	0.226
r_nbtor_refined	0.192
r_nbd_other	0.187
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.118
r_nbtor_other	0.089
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	992
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
ACORN	phasing