Experiment: 1JPK

Gly156Asp mutant of Human UroD, human uroporphyrinogen III decarboxylase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1URO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	MPD and MES, or CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.2	α = 90
b = 103.2	β = 90
c = 73.62	γ = 120

Symmetry
Space Group	P 31 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		1999-01-01	M	SINGLE WAVELENGTH

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

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	2.2	20	97.1	0.84			22708	22708		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	99.2		0.39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	1URO	2.2	20	22198	22198	1100	97.1	0.195	0.1941	0.238	0.2333	5%

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_angle_deg	2.4
x_bond_d	0.13

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2806
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing