2HDQ

AmpC beta-lactamase in complex with 2-carboxythiophene

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KE4	PDB ENTRY 1KE4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	294	1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.434	α = 90
b = 74.781	β = 116.14
c = 98.281	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 QUANTUM 210		2005-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1

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	2.1	50	91	0.089	12.8	2.5		69905

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)
	2.1	2.18	78.5		0.393	2.2	2.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1KE4	2.1	30	41236	41236	2085	90.72	0.183	0.183	0.227	RANDOM	18.107

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]
-0.54		0.48	-0.03		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.029
r_dihedral_angle_4_deg	14.137
r_dihedral_angle_3_deg	13.615
r_dihedral_angle_1_deg	6.506
r_scangle_it	2.319
r_scbond_it	1.62
r_angle_refined_deg	1.526
r_angle_other_deg	0.991
r_mcangle_it	0.965
r_mcbond_it	0.86
r_symmetry_vdw_other	0.259
r_nbd_refined	0.193
r_nbd_other	0.188
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.165
r_xyhbond_nbd_refined	0.147
r_mcbond_other	0.133
r_symmetry_hbond_refined	0.11
r_nbtor_other	0.085
r_chiral_restr	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5600
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction