Experiment: 1WUP

Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81E)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DD6	PDB ENTRY 1DD6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	297	acetic-acetate, citrate, PEG4000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.213	α = 84.81
b = 73.061	β = 76.1
c = 80.89	γ = 74

Symmetry
Space Group	P 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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	0.98	SPring-8	BL40B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.97	99				19685	19685

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.97	3.08

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DD6	3	19.73	18601	908	88.7	0.224	0.224	0.295	RANDOM	27.3

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]
-17.78	-13.37	-11.56	18.17	19.5	-0.39

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.8
c_scangle_it	5.77
c_mcangle_it	4.59
c_scbond_it	3.81
c_mcbond_it	2.83
c_angle_deg	1.6
c_improper_angle_d	0.95
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6786
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	8

Software

Software
Software Name	Purpose
DENZO	data reduction
ADDREF	data reduction
AMoRE	phasing
CNS	refinement