3NZ9 | pdb_00003nz9

Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)Pyrido[2,3-d]pyrimidine Derivatives

X-RAY DIFFRACTION

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	33-336% PEG 2K, 46-52 mM MES pH 6 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.952	α = 90
b = 42.673	β = 94.8
c = 60.099	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	1.6	50	96.6	0.028	0.042	5	3.6	24011	22779	2	2	27.9

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)
	1.6	1.66	90.3		0.33	0.113	13.1	3.2	2229

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	1.8	24.51	2	2	24011	16107	886	97.15	0.20548	0.20181	0.2	0.27184	0.27	RANDOM	28.375

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	-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.737
r_dihedral_angle_4_deg	17.939
r_dihedral_angle_3_deg	16.712
r_dihedral_angle_1_deg	6.993
r_scangle_it	4.847
r_scbond_it	3.267
r_mcangle_it	2.342
r_angle_refined_deg	2.336
r_mcbond_it	1.39
r_chiral_restr	0.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.737
r_dihedral_angle_4_deg	17.939
r_dihedral_angle_3_deg	16.712
r_dihedral_angle_1_deg	6.993
r_scangle_it	4.847
r_scbond_it	3.267
r_mcangle_it	2.342
r_angle_refined_deg	2.336
r_mcbond_it	1.39
r_chiral_restr	0.174
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1686
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	79

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.