3CIF | pdb_00003cif

Crystal Structure of C153S mutant glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CHZ	PDB ENTRY 3CHZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	298	20% PEG 3000 Prior to crystallization, the protein was incubated with 2 mM NAD and 11 mM D-L-glyceraldehyde 3-phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68	α = 90
b = 120.1	β = 92.08
c = 79.28	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	103	CCD	MAR225		2005-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	20	99.7	0.087	11.9	7.1		84846

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	2.07	99.3		0.309		6.2

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	PDB ENTRY 3CHZ	2	20	79294	4253	98.5	0.17921	0.17756	0.18	0.20973	0.21	RANDOM	21.914

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]
-0.24		0.28	0.6		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.914
r_dihedral_angle_4_deg	18.98
r_dihedral_angle_3_deg	12.228
r_dihedral_angle_1_deg	4.937
r_scangle_it	1.102
r_angle_refined_deg	0.979
r_scbond_it	0.679
r_mcangle_it	0.625
r_mcbond_it	0.354
r_nbtor_refined	0.297
r_nbd_refined	0.17
r_symmetry_vdw_refined	0.103
r_xyhbond_nbd_refined	0.095
r_symmetry_hbond_refined	0.066
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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	10072
Nucleic Acid Atoms
Solvent Atoms	723
Heterogen Atoms	230

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
CNS	refinement