2FFF

Open Form of a Class A Transpeptidase Domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BG1	PDB ENTRY 2BG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	100 mM Tris, 20% PEG MME 2000, 10 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.661	α = 90
b = 78.043	β = 113.02
c = 60.315	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		2005-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.2	39	99.5	0.106	11	3.7	27505	27505			36.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.35	96.6		2.1	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BG1	2.23	39	27505	27505	1408	99.48	0.186	0.186	0.183	0.246	RANDOM	33.373

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]
-1.02		0.43	0.31		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_3_deg	14.863
r_dihedral_angle_4_deg	14.442
r_dihedral_angle_1_deg	6.826
r_scangle_it	2.342
r_scbond_it	1.574
r_angle_refined_deg	1.326
r_mcangle_it	1.006
r_mcbond_it	0.871
r_angle_other_deg	0.824
r_symmetry_vdw_other	0.293
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.205
r_metal_ion_refined	0.2
r_symmetry_vdw_refined	0.192
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.18
r_mcbond_other	0.13
r_nbtor_other	0.084
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3616
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing