1S07

Crystal Structure of the R253A Mutant of 7,8-Diaminopelargonic Acid Synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		WT dimer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	PEG4000, MPD, HEPES, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.08	α = 90
b = 56.527	β = 96.32
c = 120.993	γ = 90

Symmetry
Space Group	P 1 21 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		2001-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.85	EMBL/DESY, HAMBURG	BW7B

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	2.42	20	90.6	0.077	14.8		29730	26936			34.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.42	2.48	55.3		0.028	24.8

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	WT dimer	2.42	20	25407	25407	1413	89.32	0.19	0.18968	0.18776	0.22414	RANDOM	28.654

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]
-1.2		0.48	2.59		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.18
r_dihedral_angle_1_deg	3.93
r_scangle_it	3.201
r_scbond_it	1.883
r_angle_refined_deg	1.654
r_mcangle_it	1.316
r_angle_other_deg	1.174
r_mcbond_it	0.697
r_symmetry_vdw_refined	0.476
r_symmetry_vdw_other	0.462
r_nbd_refined	0.276
r_nbtor_other	0.271
r_nbd_other	0.218
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_other	0.126
r_chiral_restr	0.09
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6590
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	38

Software

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