1O8C

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O89	NATIVE YHD, PDB ID CODE 1O89

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		8.5 % PEG 8K, 0.1 M NA-ACETATE PH 5.5, 0.01 MM ZNCL2, 5 MM NADPH

Crystal Properties
Matthews coefficient	Solvent content
3.4	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 189.313	α = 90
b = 189.313	β = 90
c = 98.654	γ = 120

Symmetry
Space Group	P 61

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 CCD		2002-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.6	43.7	100	0.05	8.3	6.1		62012

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)
1	2.6	2.67	100		0.192	3.9	5.9

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	NATIVE YHD, PDB ID CODE 1O89	2.6	158.11	58842	3140	100	0.173	0.171	0.19	0.202	0.22	RANDOM

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]
0.2	0.1		0.2		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.897
r_angle_refined_deg	1.226
r_angle_other_deg	0.776
r_symmetry_vdw_other	0.254
r_nbd_other	0.231
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.156
r_nbtor_other	0.082
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9752
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing