3NZB | pdb_00003nzb

Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Potent 5-(omega-carboxyl(alkyloxy)pyrido[2,-d]pyrimidine Derivatives

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CD2	PDB entry 3cd2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	273	33-36% PEG 2K, 46-52 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.86	α = 90
b = 42.709	β = 94.62
c = 60.585	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	200	CCD	MARMOSAIC 325 mm CCD	mirrors	2006-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.975	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.3	50	96	0.056	0.067	12.8	3.5	44341	40688	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.37	97.7		0.645	0.759	1.7	3.5

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 (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 3cd2	1.45	24.66	30117	30117	1629	94.79	0.24384	0.24103	0.24	0.2954	0.29	RANDOM	24.031

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]
		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.015
r_dihedral_angle_4_deg	16.208
r_dihedral_angle_3_deg	15.479
r_dihedral_angle_1_deg	7.367
r_scangle_it	4.302
r_scbond_it	3.128
r_angle_refined_deg	2.417
r_mcangle_it	2.381
r_mcbond_it	1.492
r_symmetry_hbond_refined	0.537
r_xyhbond_nbd_refined	0.429
r_nbd_refined	0.366
r_nbtor_refined	0.346
r_symmetry_vdw_refined	0.343
r_chiral_restr	0.156
r_bond_refined_d	0.025
r_gen_planes_refined	0.013
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	1686
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	114

Software

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