2CFK | pdb_00002cfk

AGAO in complex with wc5 (Ru-wire inhibitor, 5-carbon linker)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W6G	PDB ENTRY 1W6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6		THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 6.0, 800 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK, OVER THREE DAYS. 25 MG OF THE INHIBITOR (WC5) DISSOLVED IN 250 MICROLITRE ETHANOL. 1MICROLITRE OF THIS WAS ADDED TO THE 200MICROLITRE RESERVOIR. GLYCEROL WAS THEN, ADDED IN 2-3% INCREMENTS, TO THE RESERVOIR, WITH THE NEW RESERVOIR SOLUTION SUBSTITUTING THE DROP SOLUTION. THE SOAK SAT FOR 24 HOURS AT 5% GLYCEROL. THE FINAL GLYCEROL CONCENTRATION WAS 30%.

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.885	α = 90
b = 62.944	β = 112.2
c = 92.013	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	IMAGE PLATE	MARRESEARCH	OSMIC MIRRORS	2004-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.79	15	99	0.03	24.4	4.2		322625		-3	21.59

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	1.79	1.85	76.8		0.15	4.33	2.58

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1W6G	1.8	15.02	72905	3847	98.9	0.146	0.145	0.1713	0.165	0.187	RANDOM	21.96

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]
-1.71		0.14	3.04		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.261
r_scangle_it	5.76
r_scbond_it	3.95
r_mcangle_it	2.843
r_mcbond_it	1.744
r_angle_refined_deg	1.505
r_angle_other_deg	0.791
r_symmetry_vdw_other	0.308
r_nbd_other	0.251
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.184
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.083
r_nbtor_other	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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	4868
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms	167

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling