2G1H | pdb_00002g1h

Structure of E.coli FabD complexed with glycerol

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.147	α = 90
b = 83.147	β = 90
c = 164.511	γ = 90

Symmetry
Space Group	P 41 21 2

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	mirrors	2001-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	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	1.86	20	97.5	0.061	44.7		48061	48061	2.1	2.1

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	1.86	1.98	99.2

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 (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	1MLA	1.86	20	45525	45525	2436	97.41	0.2111	0.21111	0.21052	0.22	0.22213	0.23	RANDOM	26.493

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]
0.22			0.22		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	21.386
r_dihedral_angle_1_deg	7.243
r_scangle_it	3.762
r_mcangle_it	2.877
r_scbond_it	2.449
r_mcbond_it	1.86
r_angle_refined_deg	0.754
r_symmetry_hbond_refined	0.712
r_angle_other_deg	0.58
r_symmetry_vdw_refined	0.335
r_nbd_refined	0.309
r_xyhbond_nbd_other	0.272
r_nbd_other	0.25
r_xyhbond_nbd_refined	0.227
r_symmetry_vdw_other	0.225
r_chiral_restr	0.047
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_gen_planes_other	0.002
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2257
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	6

Software

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