1U17

1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.1 M potassium cacodylate pH 5.3, 2.9 M di-ammoium hydrogen phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.006	α = 90
b = 73.987	β = 99.16
c = 65.224	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	100	IMAGE PLATE	MARRESEARCH		2003-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.08	SSRL	BL7-1

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	1.7	30	99.5	0.074	8.1	3.9		40082			20.3

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)
	1.7	1.74	98.5		0.33	1	3.7

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 2NP1	1.7	30	36923	1945	96.54	0.18469	0.18469	0.18191	0.23713	RANDOM	24.646

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		-1.6	0.27		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.3
r_scangle_it	5.248
r_scbond_it	3.324
r_mcangle_it	2.334
r_angle_refined_deg	1.962
r_mcbond_it	1.313
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.214
r_chiral_restr	0.173
r_symmetry_vdw_refined	0.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.3
r_scangle_it	5.248
r_scbond_it	3.324
r_mcangle_it	2.334
r_angle_refined_deg	1.962
r_mcbond_it	1.313
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.214
r_chiral_restr	0.173
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.16
r_metal_ion_refined	0.066
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2894
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing

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 R01GM133198.