1SO3 | pdb_00001so3

Crystal structure of H136A mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7	293	16% PEG 5000, methyl ether, 100 mM BTP pH 7.0, 5 mM MgCl2, Microbatch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.116	α = 90
b = 42.059	β = 97.06
c = 91.07	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	RIGAKU RAXIS IV		2003-07-01	M	SINGLE WAVELENGTH

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

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	1.9	91.29	99.2	0.065	26		36727	36727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	91.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	91.29	36727	34888	1839	99.29	0.1501	0.1501	0.14792	0.16	0.19247	0.21	RANDOM	19.972

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]
-0.7		0.29	1.45		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.919
r_scangle_it	3.632
r_scbond_it	2.26
r_angle_other_deg	1.933
r_angle_refined_deg	1.528
r_mcangle_it	1.346
r_mcbond_it	0.773
r_symmetry_vdw_other	0.269
r_nbd_other	0.247
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.128
r_chiral_restr	0.106
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_metal_ion_refined	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	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_other
r_symmetry_hbond_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	3297
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	30

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction