4RZQ | pdb_00004rzq

Structural Analysis of Substrate, Reaction Intermediate and Product Binding in Haemophilus influenzae Biotin Carboxylase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298.15	16% PEG3350 0.2M KCl Protein was incubated with solid N1 -methoxycarbonylbiotin methyl ester for 5 days prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.197	α = 90
b = 86.197	β = 90
c = 102.364	γ = 120

Symmetry
Space Group	P 64

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 QUANTUM 315	KB MIRRORS	2013-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.98	39.72	99.9	0.056	19.5	5.6	30073	30073			27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.09	100		0.504	2.8	5.7	4385

Refinement

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-Factor (All)	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	1DV1	1.98	39.72	28578	28578	1464	99.86	0.17828	0.17828	0.17629	0.19	0.21697	0.22	RANDOM	44.666

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]
-0.11	-0.05		-0.11		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.753
r_dihedral_angle_3_deg	17.197
r_dihedral_angle_4_deg	14.18
r_dihedral_angle_1_deg	6.797
r_long_range_B_refined	5.601
r_long_range_B_other	5.601
r_scangle_other	3.79
r_scbond_it	2.725
r_scbond_other	2.724
r_mcangle_it	2.468
r_mcangle_other	2.467
r_angle_refined_deg	2.055
r_mcbond_it	1.688
r_mcbond_other	1.682
r_angle_other_deg	0.913
r_chiral_restr	0.116
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
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	3235
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	48

Software

Software
Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling