2J9G

Crystal structure of Biotin carboxylase from E. coli in complex with AMPPNP and ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV2	PDB ENTRY 1DV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1M BIS-TRIS PH 6.5, 0.2M CACL2, 45% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.17	42.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.704	α = 90
b = 112.251	β = 90
c = 121.769	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				2007-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

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	2.05	50	99.9	0.08	29.97	7		59125

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	2.05	2.12	100		0.56	4.22	6.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DV2	2.05	82.48	56070	2990	99.7	0.192	0.19	0.236	RANDOM	23.64

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]
0.46			0.87		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.132
r_dihedral_angle_4_deg	13.74
r_dihedral_angle_3_deg	12.565
r_dihedral_angle_1_deg	5.117
r_scangle_it	1.546
r_angle_refined_deg	1.064
r_scbond_it	1.032
r_angle_other_deg	0.978
r_mcangle_it	0.651
r_mcbond_it	0.603
r_symmetry_vdw_other	0.243
r_nbd_other	0.185
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.176
r_nbtor_refined	0.166
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.129
r_nbtor_other	0.08
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
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	6823
Nucleic Acid Atoms
Solvent Atoms	669
Heterogen Atoms	70

Software

Software
Software Name	Purpose
SCALEPACK	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	phasing
REFMAC	refinement