2W70 | pdb_00002w70

Crystal structure of Biotin carboxylase from E. coli in complex with the amino-thiazole-pyrimidine fragment

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J9G	PDB ENTRY 2J9G

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.234	α = 90
b = 106.215	β = 90
c = 122.635	γ = 90

Symmetry
Space Group	P 21 21 21

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	1.77	80	99.9	0.08	20.54	4.94		107085

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	1.77	1.83	99.9		0.54	2.35	4.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2J9G	1.77	20	101581	5319	99.8	0.176	0.174	0.19	0.202	RANDOM	20.85

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]
-0.23			0.54		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.748
r_dihedral_angle_4_deg	18.796
r_dihedral_angle_3_deg	12.971
r_dihedral_angle_1_deg	4.956
r_scangle_it	2.171
r_scbond_it	1.467
r_angle_other_deg	1.142
r_angle_refined_deg	1.118
r_mcangle_it	0.75
r_mcbond_it	0.683
r_symmetry_vdw_other	0.219
r_symmetry_hbond_refined	0.212
r_nbd_refined	0.194
r_nbd_other	0.181
r_nbtor_refined	0.167
r_symmetry_vdw_refined	0.119
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.112
r_nbtor_other	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	6866
Nucleic Acid Atoms
Solvent Atoms	942
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing